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Conserved domains on  [gi|2462517972|ref|XP_054221246|]
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protein RRP5 homolog isoform X2 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 80-176 9.58e-40

S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240198 [Multi-domain]  Cd Length: 100  Bit Score: 142.74  E-value: 9.58e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972   80 LCEGMRILGCVKEVNELELVISLPNGLQGFVQVTEICDAYTKKLNEQVTQEQ---PLKDLLHLPELFSPGMLVRCVVSSL 156
Cdd:cd05693      1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEeedDEEELPDLEDLFSVGQLVRCKVVSL 80

                           90       100
                   ....*....|....*....|
gi 2462517972  157 GITDRGKKSVKLSLNPKNVN 176
Cdd:cd05693     81 DKSKSGKKRIELSLEPELVN 100
S1_Rrp5_repeat_hs7 cd05699
S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 636-707 1.06e-38

S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240204 [Multi-domain]  Cd Length: 72  Bit Score: 138.76  E-value: 1.06e-38
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517972  636 GQLVDVKVLEKTKDGLEVAVLPHNIRAFLPTSHLSDHVANGPLLHHWLQAGDILHRVLCLSQSEGRVLLCRK 707
Cdd:cd05699      1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCLSNYKGRIILTKK 72
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 715-797 3.69e-38

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 137.72  E-value: 3.69e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  715 EGGQDPKNFSEIHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRML 794
Cdd:cd04461      1 KEGTLPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFL 80


                   ...
gi 2462517972  795 LSL 797
Cdd:cd04461     81 LSL 83
S1_Rrp5_repeat_hs14 cd05705
S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1321-1394 4.95e-37

S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240210 [Multi-domain]  Cd Length: 74  Bit Score: 134.06  E-value: 4.95e-37
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517972 1321 IKEGQLLRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQHSPSKKALYNKHLPEGKLLTARVLRLNHQKNLVELS 1394
Cdd:cd05705      1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1227-1298 1.99e-35

S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240209 [Multi-domain]  Cd Length: 72  Bit Score: 129.39  E-value: 1.99e-35
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517972 1227 LEEGEVAMGRVVKVTPNEGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFVPQKVVRCYILSTADNVLTLSLR 1298
Cdd:cd05704      1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKDGKYQLSLR 72
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 542-611 3.92e-35

S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 128.50  E-value: 3.92e-35
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  542 GLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 611
Cdd:cd05698      1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1_Rrp5_repeat_hs10 cd05701
S1_Rrp5_repeat_hs10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 925-993 4.29e-32

S1_Rrp5_repeat_hs10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 10 (hs10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240206  Cd Length: 69  Bit Score: 119.99  E-value: 4.29e-32
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517972  925 GSEHQAIVQHLEKSFAIASLVETGHLAAFSLTSHLNDTFRFDSEKLQVGQGVSLTLKTTEPGVTGLLLA 993
Cdd:cd05701      1 DSRHTAIVQHADKDFAIVSLATTGDLAAFPTRSHLNDTFRFDSEKLSVGQCLDVTLKDPNCLAGGPLLA 69
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 453-521 4.55e-31

S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 116.95  E-value: 4.55e-31
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517972  453 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTL 521
Cdd:cd05697      1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 1036-1105 9.75e-30

S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240207 [Multi-domain]  Cd Length: 70  Bit Score: 113.07  E-value: 9.75e-30
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1036 GDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEGTSPTTKLKVGKTVTARVIGGRDMKTFKYLP 1105
Cdd:cd05702      1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKTHRFLP 70
S1_Rrp5_repeat_hs2_sc2 cd05694
S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 183-263 3.41e-28

S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240199 [Multi-domain]  Cd Length: 74  Bit Score: 108.88  E-value: 3.41e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  183 ALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYirqknkgAKLKVGQYLNCIVEKVKGNGGVVSLSVGHSEV 262
Cdd:cd05694      1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF-------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV 73


                   .
gi 2462517972  263 S 263
Cdd:cd05694     74 S 74
S1_Rrp5_repeat_hs4 cd05696
S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 365-435 8.04e-28

S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240201 [Multi-domain]  Cd Length: 71  Bit Score: 107.73  E-value: 8.04e-28
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517972  365 GAVLDDVPVQGFFKKAGATFRLKDGVLAYARLSHLSDSKNVFNPEAFKPGNTHKCRIIDYSQMDELALLSL 435
Cdd:cd05696      1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 846-910 1.24e-27

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


The actual alignment was detected with superfamily member cd05700:

Pssm-ID: 471952  Cd Length: 65  Bit Score: 107.25  E-value: 1.24e-27
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517972  846 GMFLDLVVQEVLEDGSVVFSGGPVPDLVLKASRYHRAGQEVESGQKKKVVILNVDLLKLEVHVSL 910
Cdd:cd05700      1 GDQLKLVVQDVTEDGSVMFSGGQVSGLTVLASRYHKEGVNVTPGCKLKAVILHVDFVKSQVHVSL 65
S1_Rrp5_repeat_hs12_sc9 cd05703
S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 1149-1223 6.17e-26

S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240208 [Multi-domain]  Cd Length: 73  Bit Score: 102.65  E-value: 6.17e-26
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517972 1149 GQTVTCFLKKYNVVKKWLEveIAPDIRGRIPLLLTSLSFKVLKHPDKKFRVGQALRATVVGPDSSKTFLCLSLTG 1223
Cdd:cd05703      1 GQEVTGFVNNVSKEFVWLT--ISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSARG 73
S1_Rrp5_repeat_hs3 cd05695
S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 281-344 1.04e-25

S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


:

Pssm-ID: 240200 [Multi-domain]  Cd Length: 66  Bit Score: 101.58  E-value: 1.04e-25
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462517972  281 GLVVKAQVQKVTPFGLTLNFLTFFTGVVDFMHLDPKKA--GTYFSNQAVRACILCVHPRTRVVHLS 344
Cdd:cd05695      1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSskSTYKEGQKVRARILYVDPSTKVVGLS 66
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1601-1861 6.96e-17

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


:

Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 82.85  E-value: 6.96e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1601 RQPESA-DDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKtisfREEQEKLnvwvALLNLENMYGSQESLT 1679
Cdd:COG2956     22 GQPDKAiDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE----RDPDRAE----ALLELAQDYLKAGLLD 93

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1680 K---VFERAVQYNEP-LKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALEC 1755
Cdd:COG2956     94 RaeeLLEKLLELDPDdAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKALKL 173

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1756 LPskEHVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVihLSLAPKRMKFF 1835
Cdd:COG2956    174 DP--DCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKA--LELDPSDDLLL 249

                          250       260
                   ....*....|....*....|....*.
gi 2462517972 1836 FKRYLdYEKQHGTEKdVQAVKAKALE 1861
Cdd:COG2956    250 ALADL-LERKEGLEA-ALALLERQLR 273
PTZ00121 super family cl31754
MAEBL; Provisional
 1402-1659 1.65e-04

MAEBL; Provisional


The actual alignment was detected with superfamily member PTZ00121:

Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 47.06  E-value: 1.65e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1402 KPDVLSASLEgQLTKQEERKTEAEERDQKGEKKNQKRNEKKN----QKGQEEVempsKEKQQPQKPQAQKRGGRECRESG 1477
Cdd:PTZ00121  1379 KADAAKKKAE-EKKKADEAKKKAEEDKKKADELKKAAAAKKKadeaKKKAEEK----KKADEAKKKAEEAKKADEAKKKA 1453

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1478 SEQERVSKKPKKAGLSEEDDSLVDvyYREGKEEAEETNVLPKEKQTKPAEAPRLQLSSGFAwnvglDSLTPA-------- 1549
Cdd:PTZ00121  1454 EEAKKAEEAKKKAEEAKKADEAKK--KAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKA-----DEAKKAeeakkade 1526

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1550 LPPLAESSDSEEDEKPHQ---ATQIKKSKKERELEKQKAEKELSRIEEALMDPGRQPESADDFDRLVLSSPNSSILWLQY 1626
Cdd:PTZ00121  1527 AKKAEEAKKADEAKKAEEkkkADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKK 1606

                          250       260       270
                   ....*....|....*....|....*....|...
gi 2462517972 1627 MAFHlQATEIEKARAVAERALKTISFREEQEKL 1659
Cdd:PTZ00121  1607 MKAE-EAKKAEEAKIKAEELKKAEEEKKKVEQL 1638
 
Name Accession Description Interval E-value
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 80-176 9.58e-40

S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240198 [Multi-domain]  Cd Length: 100  Bit Score: 142.74  E-value: 9.58e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972   80 LCEGMRILGCVKEVNELELVISLPNGLQGFVQVTEICDAYTKKLNEQVTQEQ---PLKDLLHLPELFSPGMLVRCVVSSL 156
Cdd:cd05693      1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEeedDEEELPDLEDLFSVGQLVRCKVVSL 80

                           90       100
                   ....*....|....*....|
gi 2462517972  157 GITDRGKKSVKLSLNPKNVN 176
Cdd:cd05693     81 DKSKSGKKRIELSLEPELVN 100
S1_Rrp5_repeat_hs7 cd05699
S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 636-707 1.06e-38

S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240204 [Multi-domain]  Cd Length: 72  Bit Score: 138.76  E-value: 1.06e-38
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517972  636 GQLVDVKVLEKTKDGLEVAVLPHNIRAFLPTSHLSDHVANGPLLHHWLQAGDILHRVLCLSQSEGRVLLCRK 707
Cdd:cd05699      1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCLSNYKGRIILTKK 72
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 715-797 3.69e-38

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 137.72  E-value: 3.69e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  715 EGGQDPKNFSEIHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRML 794
Cdd:cd04461      1 KEGTLPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFL 80


                   ...
gi 2462517972  795 LSL 797
Cdd:cd04461     81 LSL 83
S1_Rrp5_repeat_hs14 cd05705
S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1321-1394 4.95e-37

S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240210 [Multi-domain]  Cd Length: 74  Bit Score: 134.06  E-value: 4.95e-37
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517972 1321 IKEGQLLRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQHSPSKKALYNKHLPEGKLLTARVLRLNHQKNLVELS 1394
Cdd:cd05705      1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1227-1298 1.99e-35

S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240209 [Multi-domain]  Cd Length: 72  Bit Score: 129.39  E-value: 1.99e-35
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517972 1227 LEEGEVAMGRVVKVTPNEGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFVPQKVVRCYILSTADNVLTLSLR 1298
Cdd:cd05704      1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKDGKYQLSLR 72
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 542-611 3.92e-35

S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 128.50  E-value: 3.92e-35
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  542 GLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 611
Cdd:cd05698      1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1_Rrp5_repeat_hs10 cd05701
S1_Rrp5_repeat_hs10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 925-993 4.29e-32

S1_Rrp5_repeat_hs10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 10 (hs10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240206  Cd Length: 69  Bit Score: 119.99  E-value: 4.29e-32
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517972  925 GSEHQAIVQHLEKSFAIASLVETGHLAAFSLTSHLNDTFRFDSEKLQVGQGVSLTLKTTEPGVTGLLLA 993
Cdd:cd05701      1 DSRHTAIVQHADKDFAIVSLATTGDLAAFPTRSHLNDTFRFDSEKLSVGQCLDVTLKDPNCLAGGPLLA 69
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 453-521 4.55e-31

S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 116.95  E-value: 4.55e-31
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517972  453 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTL 521
Cdd:cd05697      1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 1036-1105 9.75e-30

S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240207 [Multi-domain]  Cd Length: 70  Bit Score: 113.07  E-value: 9.75e-30
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1036 GDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEGTSPTTKLKVGKTVTARVIGGRDMKTFKYLP 1105
Cdd:cd05702      1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKTHRFLP 70
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 364-798 6.33e-29

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 123.69  E-value: 6.33e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  364 LGAVLDDVPVQG-FFKKAGATFRLK-DGVLAYARLSHlSDSKNVFNPEAFKpGNTHKCRIIDYSQMDELALLSlRTSIIE 441
Cdd:TIGR00717   95 EKAYEEGSIVEGkIVGKVKGGFIVDlNGVEAFLPGSQ-VDVKPIKDLDSLI-GKTLKFKIIKLDQKRNNIVVS-RRAYLE 171

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  442 AQYLRYHD-----IEPGAVVKGTVLTIKSYGMLVKVGeQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKK 516
Cdd:TIGR00717  172 EERSQAREellenLKEGDVVKGVVKNITDFGAFVDLG-GVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGR 250

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  517 LMMTLKKTL------IESKLPvitcyadakPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELS-TEYIPDPERVFYTG 589
Cdd:TIGR00717  251 ISLSLKQLGedpweaIEKKFP---------VGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKG 321

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  590 QVVKVVVLNCEPSKERMLLSFKlSSDPEP-----KKEPAGhSQKKGKAINIGQLVDVKVLEKTKDGLevavlphnirafl 664
Cdd:TIGR00717  322 DEVEVMILDIDPERRRLSLGLK-QCKANPweqfeEKHPVG-DRVTGKIKKITDFGAFVELEGGIDGL------------- 386

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  665 ptSHLSD--HVANGPLLHHWLQAGDILHR-VLCLSQSEGRVLLCRKPALVSTVEggqdpkNFSEIHP-GMLLIGFVKSIK 740
Cdd:TIGR00717  387 --IHLSDisWDKDGREADHLYKKGDEIEAvVLAVDKEKKRISLGVKQLTENPWE------KFAAKYKvGSVVKGKVTEIK 458

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462517972  741 DYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:TIGR00717  459 DFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
S1_Rrp5_repeat_hs2_sc2 cd05694
S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 183-263 3.41e-28

S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240199 [Multi-domain]  Cd Length: 74  Bit Score: 108.88  E-value: 3.41e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  183 ALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYirqknkgAKLKVGQYLNCIVEKVKGNGGVVSLSVGHSEV 262
Cdd:cd05694      1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF-------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV 73


                   .
gi 2462517972  263 S 263
Cdd:cd05694     74 S 74
S1_Rrp5_repeat_hs4 cd05696
S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 365-435 8.04e-28

S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240201 [Multi-domain]  Cd Length: 71  Bit Score: 107.73  E-value: 8.04e-28
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517972  365 GAVLDDVPVQGFFKKAGATFRLKDGVLAYARLSHLSDSKNVFNPEAFKPGNTHKCRIIDYSQMDELALLSL 435
Cdd:cd05696      1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71
S1_Rrp5_repeat_hs9 cd05700
S1_Rrp5_repeat_hs9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 846-910 1.24e-27

S1_Rrp5_repeat_hs9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes Homo sapiens S1 repeat 9 (hs9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240205  Cd Length: 65  Bit Score: 107.25  E-value: 1.24e-27
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517972  846 GMFLDLVVQEVLEDGSVVFSGGPVPDLVLKASRYHRAGQEVESGQKKKVVILNVDLLKLEVHVSL 910
Cdd:cd05700      1 GDQLKLVVQDVTEDGSVMFSGGQVSGLTVLASRYHKEGVNVTPGCKLKAVILHVDFVKSQVHVSL 65
S1_Rrp5_repeat_hs12_sc9 cd05703
S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 1149-1223 6.17e-26

S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240208 [Multi-domain]  Cd Length: 73  Bit Score: 102.65  E-value: 6.17e-26
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517972 1149 GQTVTCFLKKYNVVKKWLEveIAPDIRGRIPLLLTSLSFKVLKHPDKKFRVGQALRATVVGPDSSKTFLCLSLTG 1223
Cdd:cd05703      1 GQEVTGFVNNVSKEFVWLT--ISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSARG 73
S1_Rrp5_repeat_hs3 cd05695
S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 281-344 1.04e-25

S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240200 [Multi-domain]  Cd Length: 66  Bit Score: 101.58  E-value: 1.04e-25
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462517972  281 GLVVKAQVQKVTPFGLTLNFLTFFTGVVDFMHLDPKKA--GTYFSNQAVRACILCVHPRTRVVHLS 344
Cdd:cd05695      1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSskSTYKEGQKVRARILYVDPSTKVVGLS 66
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 450-798 1.61e-25

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 113.72  E-value: 1.61e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  450 IEPGAVVKGTVLTIKSYGMLVKVGeQMRGLVppmHLADILMK---NPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTL- 525
Cdd:PRK06299   199 LEEGQVVEGVVKNITDYGAFVDLG-GVDGLL---HITDISWKrvnHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGe 274

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  526 -----IESKLPVitcyadakpglqthGFIIRVK-----DYGCIVKFYNNVQGLVpkH--ELS-TEYIPDPERVFYTGQVV 592
Cdd:PRK06299   275 dpweaIEKKYPV--------------GSKVKGKvtnitDYGAFVELEEGIEGLV--HvsEMSwTKKNKHPSKVVSVGQEV 338

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  593 KVVVLNCEPSKERMLLSFK-LSSDPE---PKKEPAGhSQKKGKAINIgqlvdvkvlekTKDGLEVAvLPHNIRAFLptsH 668
Cdd:PRK06299   339 EVMVLEIDEEKRRISLGLKqCKENPWeefAEKYPVG-DVVEGKVKNI-----------TDFGAFVG-LEGGIDGLV---H 402

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  669 LSD--HVANG--PLLHhwLQAGDILH-RVLCLSQSEGRVLLCRKPALvstveggQDP-KNFSEIHP-GMLLIGFVKSIKD 741
Cdd:PRK06299   403 LSDisWDKKGeeAVEL--YKKGDEVEaVVLKVDVEKERISLGIKQLE-------EDPfEEFAKKHKkGSIVTGTVTEVKD 473

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2462517972  742 YGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:PRK06299   474 KGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIK 530
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 180-611 2.78e-22

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 100.50  E-value: 2.78e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  180 SAEALKPGMLLTGTVSSLEDHGYLVDIG--VDGtraFLPLlkaqEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSv 257
Cdd:COG0539     12 SLKELKEGDIVKGTVVSIDDDEVLVDIGykSEG---IIPL----SEFSDEPGELEVKVGDEVEVYVEKVEDGEGEIVLS- 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  258 ghsevsTAIATEQQSWN-----LNNllpGLVVKAQVQKVTPFGLTlnfltfftgvVDFMHldpkkagtyfsnqaVRAcil 332
Cdd:COG0539     84 ------KKKADREKAWEeleeaFEN---GEPVEGKVKGVVKGGLI----------VDIGG--------------VRA--- 127

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  333 cvhprtrvvhlslrpiFLqPGrpltrlscqnlgavlddvpvqgffkkagatfrlkdgvlayarlSHLsDSKNVFNPEAFK 412
Cdd:COG0539    128 ----------------FL-PA-------------------------------------------SQV-DVRPVRDLDEYV 146

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  413 pGNTHKCRIIDYSQMDELALLSlRTSIIEAQYLR-----YHDIEPGAVVKGTVLTIKSYGMLVKVGEqMRGLVppmHLAD 487
Cdd:COG0539    147 -GKTLEFKIIKLDRKRNNVVVS-RRAVLEEEREEkreelLEKLEEGDVVEGTVKNITDFGAFVDLGG-VDGLL---HISE 220

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  488 IL---MKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTL------IESKLPVitcyadakpGLQTHGFIIRVKDYGCI 558
Cdd:COG0539    221 ISwgrVKHPSEVLKVGDEVEVKVLKIDREKERISLSLKQLQpdpwenIAEKYPV---------GDVVKGKVTRLTDFGAF 291

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2462517972  559 VKFYNNVQGLVPKHELS-TEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 611
Cdd:COG0539    292 VELEPGVEGLVHISEMSwTKRVAHPSDVVKVGDEVEVKVLDIDPEERRISLSIK 345
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1601-1861 6.96e-17

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 82.85  E-value: 6.96e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1601 RQPESA-DDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKtisfREEQEKLnvwvALLNLENMYGSQESLT 1679
Cdd:COG2956     22 GQPDKAiDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE----RDPDRAE----ALLELAQDYLKAGLLD 93

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1680 K---VFERAVQYNEP-LKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALEC 1755
Cdd:COG2956     94 RaeeLLEKLLELDPDdAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKALKL 173

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1756 LPskEHVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVihLSLAPKRMKFF 1835
Cdd:COG2956    174 DP--DCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKA--LELDPSDDLLL 249

                          250       260
                   ....*....|....*....|....*.
gi 2462517972 1836 FKRYLdYEKQHGTEKdVQAVKAKALE 1861
Cdd:COG2956    250 ALADL-LERKEGLEA-ALALLERQLR 273
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
451-522 4.47e-16

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 74.56  E-value: 4.47e-16
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517972   451 EPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLK 522
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
728-798 3.46e-15

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 71.87  E-value: 3.46e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517972   728 PGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
540-611 5.43e-15

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 71.48  E-value: 5.43e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517972   540 KPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 611
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1035-1094 8.62e-11

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 59.54  E-value: 8.62e-11
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  1035 IGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIG 1094
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVK--DPEEVLKVGDEVKVKVLS 59
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 547-609 1.01e-09

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 56.53  E-value: 1.01e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462517972  547 GFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLS 609
Cdd:pfam00575    9 GEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILS 71
PRK08059 PRK08059
general stress protein 13; Validated
 450-524 1.61e-09

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 57.36  E-value: 1.61e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517972  450 IEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKT 524
Cdd:PRK08059     5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRAT 79
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1228-1298 1.98e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 52.61  E-value: 1.98e-08
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462517972  1228 EEGEVAMGRVVKVTPNeGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFVPQKVVRCYILS--TADNVLTLSLR 1298
Cdd:smart00316    1 EVGDVVEGTVTEITPG-GAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSvdEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1322-1395 4.32e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 51.84  E-value: 4.32e-08
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517972  1322 KEGQLLRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQHSPSKKalyNKHLPEGKLLTARVLRLNHQKNLVELSF 1395
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDP---EEVLKVGDEVKVKVLSVDEEKGRIILSL 71
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 451-517 1.32e-07

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 50.36  E-value: 1.32e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462517972  451 EPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKL 517
Cdd:pfam00575    2 EKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRI 68
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 729-797 2.70e-07

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 49.59  E-value: 2.70e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517972  729 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSL 797
Cdd:pfam00575    4 GDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 728-798 4.35e-07

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 53.29  E-value: 4.35e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517972  728 PGMLLIGFVKSIKDYGVFI---QFPsGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:PRK03987     8 EGELVVGTVKEVKDFGAFVtldEYP-GKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLK 80
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
185-256 1.47e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 47.60  E-value: 1.47e-06
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517972   185 KPGMLLTGTVSSLEDHGYLVDIGvDGTRAFLPLLKAQEYiRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLS 256
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLG-NGVEGLIPISELSDK-RVKDPEEVLKVGDEVKVKVLSVDEEKGRIILS 70
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
378-436 5.95e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 45.67  E-value: 5.95e-06
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517972   378 KKAGATFRLKDGVLAYARLSHLSDSKNVFNPEAFKPGNTHKCRIIDYSQMDELALLSLR 436
Cdd:smart00316   14 TPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1147-1221 1.12e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 44.90  E-value: 1.12e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517972  1147 QAGQTVTCFLKkyNVVKKWLEVEIAPDIRGRIPLllTSLSFKVLKHPDKKFRVGQALRATVVGPDSSKTFLCLSL 1221
Cdd:smart00316    1 EVGDVVEGTVT--EITPGGAFVDLGNGVEGLIPI--SELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
82-170 2.52e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 43.75  E-value: 2.52e-05
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972    82 EGMRILGCVKEVNELELVISLPNGLQGFVQVTEICDAYTKKLNEQvtqeqplkdllhlpelFSPGMLVRCVVSSLgitDR 161
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEV----------------LKVGDEVKVKVLSV---DE 62


                    ....*....
gi 2462517972   162 GKKSVKLSL 170
Cdd:smart00316   63 EKGRIILSL 71
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 449-508 3.45e-05

Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 45.17  E-value: 3.45e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462517972  449 DIEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVppmH---LADILMKNPEKKYHIGDEVKCRVL 508
Cdd:COG1098      2 SIEVGDIVEGKVTGITPFGAFVELPEGTTGLV---HiseIADGYVKDINDYLKVGDEVKVKVL 61
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
634-707 5.25e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 42.98  E-value: 5.25e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517972   634 NIGQLVDVKVLEKTKDGLEVAvLPHNIRAFLPTSHLSDHvaNGPLLHHWLQAGDILH-RVLCLSQSEGRVLLCRK 707
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVD-LGNGVEGLIPISELSDK--RVKDPEEVLKVGDEVKvKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
280-346 5.68e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 42.98  E-value: 5.68e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517972   280 PGLVVKAQVQKVTPFGLTLNFLTFFTGVVDFMHLDPKKAG----TYFSNQAVRACILCVHPRTRVVHLSLR 346
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKdpeeVLKVGDEVKVKVLSVDEEKGRIILSLK 72
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 547-629 8.52e-05

Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 44.01  E-value: 8.52e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  547 GFIIRVKDYGCIVKFYNNVQGLVpkH--ELSTEYIPDPERVFYTGQVVKVVVLNCEPSKeRMLLSFK-LSSDPEPKKEPA 623
Cdd:COG1098     11 GKVTGITPFGAFVELPEGTTGLV--HisEIADGYVKDINDYLKVGDEVKVKVLSIDEDG-KISLSIKqAEEKPKRPPRPR 87


                   ....*.
gi 2462517972  624 GHSQKK 629
Cdd:COG1098     88 RNSRPK 93
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 1035-1094 1.09e-04

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 42.27  E-value: 1.09e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1035 IGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIG 1094
Cdd:pfam00575    3 KGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVE--DPDEVIKVGDEVKVKVLK 60
PRK08059 PRK08059
general stress protein 13; Validated
 552-629 1.31e-04

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 43.50  E-value: 1.31e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517972  552 VKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFKLSSD-PEPKKEPAGHSQKK 629
Cdd:PRK08059    18 IQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEEaPEAKRKKGKILIPN 96
Suf pfam05843
Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of ...
 1728-1870 1.41e-04

Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of forked (Suf) like proteins. The Drosophila melanogaster Suppressor of forked [Su(f)] protein shares homology with the yeast RNA14 protein and the 77-kDa subunit of human cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilization and an important role of the GU-rich sequence for this regulation to occur.


Pssm-ID: 428647 [Multi-domain]  Cd Length: 291  Bit Score: 45.83  E-value: 1.41e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1728 VWIKYGAFLlRRSQAAASHR-VLQRALEclpsKEHV--DVIAKFAQLEFQLG-DAERAKAIFENTLSTYPKRTDVWSVYI 1803
Cdd:pfam05843    3 VWIQYMRAM-RRAEGIKGARkVFKKARK----RPRLtyHVYVASALMEYYCSkDPAVAFKIFELGLKLFPEDEEFVLKYL 77

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462517972 1804 DMTIKHGSQKDVRDIFERVIHlSLAPKRM-KFFFKRYLDYEKQHGTEKDVQAVKAKALEYVEAKSSVL 1870
Cdd:pfam05843   78 DYLISLNDDNNARVLFERVLT-RLAQEKEaKPLWKKFISYESTFGDLASILKLEKRMAELFPEDPPLA 144
PTZ00121 PTZ00121
MAEBL; Provisional
 1402-1659 1.65e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 47.06  E-value: 1.65e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1402 KPDVLSASLEgQLTKQEERKTEAEERDQKGEKKNQKRNEKKN----QKGQEEVempsKEKQQPQKPQAQKRGGRECRESG 1477
Cdd:PTZ00121  1379 KADAAKKKAE-EKKKADEAKKKAEEDKKKADELKKAAAAKKKadeaKKKAEEK----KKADEAKKKAEEAKKADEAKKKA 1453

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1478 SEQERVSKKPKKAGLSEEDDSLVDvyYREGKEEAEETNVLPKEKQTKPAEAPRLQLSSGFAwnvglDSLTPA-------- 1549
Cdd:PTZ00121  1454 EEAKKAEEAKKKAEEAKKADEAKK--KAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKA-----DEAKKAeeakkade 1526

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1550 LPPLAESSDSEEDEKPHQ---ATQIKKSKKERELEKQKAEKELSRIEEALMDPGRQPESADDFDRLVLSSPNSSILWLQY 1626
Cdd:PTZ00121  1527 AKKAEEAKKADEAKKAEEkkkADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKK 1606

                          250       260       270
                   ....*....|....*....|....*....|...
gi 2462517972 1627 MAFHlQATEIEKARAVAERALKTISFREEQEKL 1659
Cdd:PTZ00121  1607 MKAE-EAKKAEEAKIKAEELKKAEEEKKKVEQL 1638
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
1033-1093 2.59e-04

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 42.38  E-value: 2.59e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517972 1033 LSIGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHI----LDDVPEgtspttKLKVGKTVTARVI 1093
Cdd:PRK07252     1 MKIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIktgfIDNIHQ------LLKVGEEVLVQVV 59
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 170-307 8.89e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 43.71  E-value: 8.89e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  170 LNPKNVNRVLSAEA----------------LKPGMLLTGTVSSLEDHGYLVDIG-VDGtraflpLLKAQE--YIRQKNKG 230
Cdd:PRK06676   160 LDPEKNRVILSRRAvveeeraakkeellssLKEGDVVEGTVARLTDFGAFVDIGgVDG------LVHISElsHERVEKPS 233

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517972  231 AKLKVGQYLNCIVEKVKGNGGVVSLSVGhsevstaiATEQQSWNL--NNLLPGLVVKAQVQKVTPFGLtlnFLTFFTGV 307
Cdd:PRK06676   234 EVVSVGQEVEVKVLSIDWETERISLSLK--------DTLPGPWEGveEKLPEGDVIEGTVKRLTDFGA---FVEVLPGV 301
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 1499-1794 1.51e-03

putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.


Pssm-ID: 274350 [Multi-domain]  Cd Length: 899  Bit Score: 43.53  E-value: 1.51e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1499 LVDVYYREGKEEaEETNVLPKEKQTKPAE-APRLQLSSGFawnVGLDSLTPALPPLAESSDSEEDEKphQATQIKKSKke 1577
Cdd:TIGR02917  539 LAGLYLRTGNEE-EAVAWLEKAAELNPQEiEPALALAQYY---LGKGQLKKALAILNEAADAAPDSP--EAWLMLGRA-- 610

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1578 relekQKAEKELSRIEEAlmdpgrqpesaddFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTIS-FREEQ 1656
Cdd:TIGR02917  611 -----QLAAGDLNKAVSS-------------FKKLLALQPDSALALLLLADAYAVMKNYAKAITSLKRALELKPdNTEAQ 672

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1657 EKLnvwVALLNLENMYGSQESLTKVFEraVQYNEPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVwIKYGAFL 1736
Cdd:TIGR02917  673 IGL---AQLLLAAKRTESAKKIAKSLQ--KQHPKAALGFELEGDLYLRQKDYPAAIQAYRKALKRAPSSQNA-IKLHRAL 746

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517972 1737 LRRSQAAASHRVLQRALeclpsKEHV-DVIAKFAQLEFQLGDAERAKAI--FENTLSTYPK 1794
Cdd:TIGR02917  747 LASGNTAEAVKTLEAWL-----KTHPnDAVLRTALAELYLAQKDYDKAIkhYQTVVKKAPD 802
DUF612 pfam04747
Protein of unknown function, DUF612; This family includes several uncharacterized proteins ...
 1399-1599 5.16e-03

Protein of unknown function, DUF612; This family includes several uncharacterized proteins from Caenorhabditis elegans.


Pssm-ID: 282585 [Multi-domain]  Cd Length: 511  Bit Score: 41.59  E-value: 5.16e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1399 DTGKPDVLSASLEGQLTKQEERKTEAEERDQKGEKKNQKRNEKKNQKGQEEVEMPSKEKQQPQKPQAQkrggRECRESGS 1478
Cdd:pfam04747   49 DQRKEAFASLELTEQPQQVEKVKKSEKKKAQKQIAKDHEAEQKVNAKKAAEKEARRAEAEAKKRAAQE----EEHKQWKA 124

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1479 EQERVSKKPKKaglseEDDSLVDVYYREGKEEAEETNVLPKEKQTKPAEAPRLQLSSGFAWNVGLD-SLTPALPPLAESS 1557
Cdd:pfam04747  125 EQERIQKEQEK-----KEADLKKLQAEKKKEKAVKAEKAEKAEKTKKASTPAPVEEEIVVKKVANDrSAAPAPEPKTPTN 199

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 2462517972 1558 DSEEDEKPHQATQIKKSKKERELEKQKAEKELSRIEEALMDP 1599
Cdd:pfam04747  200 TPAEPAEQVQEITGKKNKKNKKKSESEATAAPASVEQVVEQP 241
 
Name Accession Description Interval E-value
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 80-176 9.58e-40

S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240198 [Multi-domain]  Cd Length: 100  Bit Score: 142.74  E-value: 9.58e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972   80 LCEGMRILGCVKEVNELELVISLPNGLQGFVQVTEICDAYTKKLNEQVTQEQ---PLKDLLHLPELFSPGMLVRCVVSSL 156
Cdd:cd05693      1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTERLEELDEESEeedDEEELPDLEDLFSVGQLVRCKVVSL 80

                           90       100
                   ....*....|....*....|
gi 2462517972  157 GITDRGKKSVKLSLNPKNVN 176
Cdd:cd05693     81 DKSKSGKKRIELSLEPELVN 100
S1_Rrp5_repeat_hs7 cd05699
S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 636-707 1.06e-38

S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240204 [Multi-domain]  Cd Length: 72  Bit Score: 138.76  E-value: 1.06e-38
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517972  636 GQLVDVKVLEKTKDGLEVAVLPHNIRAFLPTSHLSDHVANGPLLHHWLQAGDILHRVLCLSQSEGRVLLCRK 707
Cdd:cd05699      1 GKLVDARVLKKTLNGLEVAILPEEIRAFLPTMHLSDHVSNCPLLWHCLQEGDTIPNLMCLSNYKGRIILTKK 72
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 715-797 3.69e-38

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 137.72  E-value: 3.69e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  715 EGGQDPKNFSEIHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRML 794
Cdd:cd04461      1 KEGTLPTNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFL 80


                   ...
gi 2462517972  795 LSL 797
Cdd:cd04461     81 LSL 83
S1_Rrp5_repeat_hs14 cd05705
S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1321-1394 4.95e-37

S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240210 [Multi-domain]  Cd Length: 74  Bit Score: 134.06  E-value: 4.95e-37
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517972 1321 IKEGQLLRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQHSPSKKALYNKHLPEGKLLTARVLRLNHQKNLVELS 1394
Cdd:cd05705      1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSLYNKYLPEGKLLTAKVLSVNSEKNLVELS 74
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1227-1298 1.99e-35

S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240209 [Multi-domain]  Cd Length: 72  Bit Score: 129.39  E-value: 1.99e-35
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517972 1227 LEEGEVAMGRVVKVTPNEGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFVPQKVVRCYILSTADNVLTLSLR 1298
Cdd:cd05704      1 LEEGAVTLGMVTKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCILSKKDGKYQLSLR 72
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 542-611 3.92e-35

S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 128.50  E-value: 3.92e-35
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  542 GLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 611
Cdd:cd05698      1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
S1_Rrp5_repeat_hs10 cd05701
S1_Rrp5_repeat_hs10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 925-993 4.29e-32

S1_Rrp5_repeat_hs10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 10 (hs10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240206  Cd Length: 69  Bit Score: 119.99  E-value: 4.29e-32
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517972  925 GSEHQAIVQHLEKSFAIASLVETGHLAAFSLTSHLNDTFRFDSEKLQVGQGVSLTLKTTEPGVTGLLLA 993
Cdd:cd05701      1 DSRHTAIVQHADKDFAIVSLATTGDLAAFPTRSHLNDTFRFDSEKLSVGQCLDVTLKDPNCLAGGPLLA 69
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 453-521 4.55e-31

S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 116.95  E-value: 4.55e-31
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517972  453 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTL 521
Cdd:cd05697      1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 1036-1105 9.75e-30

S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240207 [Multi-domain]  Cd Length: 70  Bit Score: 113.07  E-value: 9.75e-30
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1036 GDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEGTSPTTKLKVGKTVTARVIGGRDMKTFKYLP 1105
Cdd:cd05702      1 GDLVKAKVKSVKPTQLNVQLADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIGGHDAKTHRFLP 70
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 364-798 6.33e-29

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 123.69  E-value: 6.33e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  364 LGAVLDDVPVQG-FFKKAGATFRLK-DGVLAYARLSHlSDSKNVFNPEAFKpGNTHKCRIIDYSQMDELALLSlRTSIIE 441
Cdd:TIGR00717   95 EKAYEEGSIVEGkIVGKVKGGFIVDlNGVEAFLPGSQ-VDVKPIKDLDSLI-GKTLKFKIIKLDQKRNNIVVS-RRAYLE 171

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  442 AQYLRYHD-----IEPGAVVKGTVLTIKSYGMLVKVGeQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKK 516
Cdd:TIGR00717  172 EERSQAREellenLKEGDVVKGVVKNITDFGAFVDLG-GVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGR 250

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  517 LMMTLKKTL------IESKLPvitcyadakPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELS-TEYIPDPERVFYTG 589
Cdd:TIGR00717  251 ISLSLKQLGedpweaIEKKFP---------VGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwVKKNSHPSKVVKKG 321

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  590 QVVKVVVLNCEPSKERMLLSFKlSSDPEP-----KKEPAGhSQKKGKAINIGQLVDVKVLEKTKDGLevavlphnirafl 664
Cdd:TIGR00717  322 DEVEVMILDIDPERRRLSLGLK-QCKANPweqfeEKHPVG-DRVTGKIKKITDFGAFVELEGGIDGL------------- 386

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  665 ptSHLSD--HVANGPLLHHWLQAGDILHR-VLCLSQSEGRVLLCRKPALVSTVEggqdpkNFSEIHP-GMLLIGFVKSIK 740
Cdd:TIGR00717  387 --IHLSDisWDKDGREADHLYKKGDEIEAvVLAVDKEKKRISLGVKQLTENPWE------KFAAKYKvGSVVKGKVTEIK 458

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462517972  741 DYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:TIGR00717  459 DFGAFVELPGGVEGLIRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
S1_Rrp5_repeat_hs2_sc2 cd05694
S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 183-263 3.41e-28

S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240199 [Multi-domain]  Cd Length: 74  Bit Score: 108.88  E-value: 3.41e-28
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  183 ALKPGMLLTGTVSSLEDHGYLVDIGVDGTRAFLPLLKAQEYirqknkgAKLKVGQYLNCIVEKVKGNGGVVSLSVGHSEV 262
Cdd:cd05694      1 DLVEGMVLSGCVSSVEDHGYILDIGIPGTTGFLPKKDAGNF-------SKLKVGQLLLCVVEKVKDDGRVVSLSADPSKV 73


                   .
gi 2462517972  263 S 263
Cdd:cd05694     74 S 74
S1_Rrp5_repeat_hs4 cd05696
S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 365-435 8.04e-28

S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240201 [Multi-domain]  Cd Length: 71  Bit Score: 107.73  E-value: 8.04e-28
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517972  365 GAVLDDVPVQGFFKKAGATFRLKDGVLAYARLSHLSDSKNVFNPEAFKPGNTHKCRIIDYSQMDELALLSL 435
Cdd:cd05696      1 GAVVDSVKVTKVEPDLGAVFELKDGLLGFVHISHLSDDKVPSDTGPFKAGTTHKARIIGYSPMDGLLQLSL 71
S1_Rrp5_repeat_hs9 cd05700
S1_Rrp5_repeat_hs9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 846-910 1.24e-27

S1_Rrp5_repeat_hs9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes Homo sapiens S1 repeat 9 (hs9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240205  Cd Length: 65  Bit Score: 107.25  E-value: 1.24e-27
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517972  846 GMFLDLVVQEVLEDGSVVFSGGPVPDLVLKASRYHRAGQEVESGQKKKVVILNVDLLKLEVHVSL 910
Cdd:cd05700      1 GDQLKLVVQDVTEDGSVMFSGGQVSGLTVLASRYHKEGVNVTPGCKLKAVILHVDFVKSQVHVSL 65
S1_Rrp5_repeat_hs12_sc9 cd05703
S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 1149-1223 6.17e-26

S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240208 [Multi-domain]  Cd Length: 73  Bit Score: 102.65  E-value: 6.17e-26
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517972 1149 GQTVTCFLKKYNVVKKWLEveIAPDIRGRIPLLLTSLSFKVLKHPDKKFRVGQALRATVVGPDSSKTFLCLSLTG 1223
Cdd:cd05703      1 GQEVTGFVNNVSKEFVWLT--ISPDVKGRIPLLDLSDDVSVLEHPEKKFPIGQALKAKVVGVDKEHKLLRLSARG 73
S1_Rrp5_repeat_hs3 cd05695
S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 281-344 1.04e-25

S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240200 [Multi-domain]  Cd Length: 66  Bit Score: 101.58  E-value: 1.04e-25
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462517972  281 GLVVKAQVQKVTPFGLTLNFLTFFTGVVDFMHLDPKKA--GTYFSNQAVRACILCVHPRTRVVHLS 344
Cdd:cd05695      1 GMLVNARVKKVLSNGLILDFLSSFTGTVDFLHLDPEKSskSTYKEGQKVRARILYVDPSTKVVGLS 66
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 450-798 1.61e-25

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 113.72  E-value: 1.61e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  450 IEPGAVVKGTVLTIKSYGMLVKVGeQMRGLVppmHLADILMK---NPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTL- 525
Cdd:PRK06299   199 LEEGQVVEGVVKNITDYGAFVDLG-GVDGLL---HITDISWKrvnHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLKQLGe 274

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  526 -----IESKLPVitcyadakpglqthGFIIRVK-----DYGCIVKFYNNVQGLVpkH--ELS-TEYIPDPERVFYTGQVV 592
Cdd:PRK06299   275 dpweaIEKKYPV--------------GSKVKGKvtnitDYGAFVELEEGIEGLV--HvsEMSwTKKNKHPSKVVSVGQEV 338

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  593 KVVVLNCEPSKERMLLSFK-LSSDPE---PKKEPAGhSQKKGKAINIgqlvdvkvlekTKDGLEVAvLPHNIRAFLptsH 668
Cdd:PRK06299   339 EVMVLEIDEEKRRISLGLKqCKENPWeefAEKYPVG-DVVEGKVKNI-----------TDFGAFVG-LEGGIDGLV---H 402

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  669 LSD--HVANG--PLLHhwLQAGDILH-RVLCLSQSEGRVLLCRKPALvstveggQDP-KNFSEIHP-GMLLIGFVKSIKD 741
Cdd:PRK06299   403 LSDisWDKKGeeAVEL--YKKGDEVEaVVLKVDVEKERISLGIKQLE-------EDPfEEFAKKHKkGSIVTGTVTEVKD 473

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2462517972  742 YGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:PRK06299   474 KGAFVELEDGVEGLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIK 530
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 180-611 2.78e-22

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 100.50  E-value: 2.78e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  180 SAEALKPGMLLTGTVSSLEDHGYLVDIG--VDGtraFLPLlkaqEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSv 257
Cdd:COG0539     12 SLKELKEGDIVKGTVVSIDDDEVLVDIGykSEG---IIPL----SEFSDEPGELEVKVGDEVEVYVEKVEDGEGEIVLS- 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  258 ghsevsTAIATEQQSWN-----LNNllpGLVVKAQVQKVTPFGLTlnfltfftgvVDFMHldpkkagtyfsnqaVRAcil 332
Cdd:COG0539     84 ------KKKADREKAWEeleeaFEN---GEPVEGKVKGVVKGGLI----------VDIGG--------------VRA--- 127

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  333 cvhprtrvvhlslrpiFLqPGrpltrlscqnlgavlddvpvqgffkkagatfrlkdgvlayarlSHLsDSKNVFNPEAFK 412
Cdd:COG0539    128 ----------------FL-PA-------------------------------------------SQV-DVRPVRDLDEYV 146

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  413 pGNTHKCRIIDYSQMDELALLSlRTSIIEAQYLR-----YHDIEPGAVVKGTVLTIKSYGMLVKVGEqMRGLVppmHLAD 487
Cdd:COG0539    147 -GKTLEFKIIKLDRKRNNVVVS-RRAVLEEEREEkreelLEKLEEGDVVEGTVKNITDFGAFVDLGG-VDGLL---HISE 220

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  488 IL---MKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTL------IESKLPVitcyadakpGLQTHGFIIRVKDYGCI 558
Cdd:COG0539    221 ISwgrVKHPSEVLKVGDEVEVKVLKIDREKERISLSLKQLQpdpwenIAEKYPV---------GDVVKGKVTRLTDFGAF 291

                          410       420       430       440       450
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2462517972  559 VKFYNNVQGLVPKHELS-TEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 611
Cdd:COG0539    292 VELEPGVEGLVHISEMSwTKRVAHPSDVVKVGDEVEVKVLDIDPEERRISLSIK 345
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 182-611 2.61e-20

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 97.11  E-value: 2.61e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  182 EALKPGMLLTGTVSSLEDHGYLVDIGvdGTRAFLPlLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSVGHse 261
Cdd:TIGR00717  183 ENLKEGDVVKGVVKNITDFGAFVDLG--GVDGLLH-ITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQ-- 257

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  262 vstaiaTEQQSWN--LNNLLPGLVVKAQVQKVTPFGltlnfltfftgvvdfmhldpkkagtyfsnqavracilcvhprtr 339
Cdd:TIGR00717  258 ------LGEDPWEaiEKKFPVGDKITGRVTNLTDYG-------------------------------------------- 287

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  340 vvhlslrpIFLQpgrpltrlscqnlgavlddvpvqgffkkagatfrLKDGVLAYARLSHLSDSKNVFNP-EAFKPGNTHK 418
Cdd:TIGR00717  288 --------VFVE----------------------------------IEEGIEGLVHVSEMSWVKKNSHPsKVVKKGDEVE 325

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  419 CRIIDYSQMDELALLSLRT------SIIEAQYlryhdiEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVppmHLADIL--- 489
Cdd:TIGR00717  326 VMILDIDPERRRLSLGLKQckanpwEQFEEKH------PVGDRVTGKIKKITDFGAFVELEGGIDGLI---HLSDISwdk 396

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  490 -MKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKtLIESKLPVITcyADAKPGLQTHGFIIRVKDYGCIVKFYNNVQGL 568
Cdd:TIGR00717  397 dGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQ-LTENPWEKFA--AKYKVGSVVKGKVTEIKDFGAFVELPGGVEGL 473

                          410       420       430       440
                   ....*....|....*....|....*....|....*....|...
gi 2462517972  569 VPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 611
Cdd:TIGR00717  474 IRNSELSENRDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
427-798 4.07e-20

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 96.94  E-value: 4.07e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  427 MDELALLSLRTSIIEAQYLRYHDIEP--GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVK 504
Cdd:PRK00087   275 MSELDNMEEVEENEQLEYMNELEKQIrrGDIVKGTVVSVNENEVFVDVGYKSEGVIPLRELTLDEISSLKESVKVGDEIE 354

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  505 CRVLLCD------------PEAKKLMMTLKKTLiESKLPVItcyadakpglqthGFIIRVKDYGCIVKfYNNVQGLVPKH 572
Cdd:PRK00087   355 VKVLKLEdedgyvvlskkeADREKAWKELEEAF-ENGEPVK-------------GKVKEVVKGGLLVD-YGGVRAFLPAS 419

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  573 ELSTEYIPDPERvfYTGQVVKVVVLNCEPSKERMLLsfkLSSDPEPKKEPAGHSQKKGKAINIGQLVDVKVLEKTKDGLE 652
Cdd:PRK00087   420 HVELGYVEDLSE--YKGQELEVKIIEFNRKRRKKVV---LSRKAILEEEKEKKKEETWNSLEEGDVVEGEVKRLTDFGAF 494

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  653 VAVlpHNIRAFLPTSHLSDHVANGPLLHhwLQAGDILH-RVLCLSQSEGRVLLCRKPALvstveggQDP-KNFSEIHP-G 729
Cdd:PRK00087   495 VDI--GGVDGLLHVSEISWGRVEKPSDV--LKVGDEIKvYILDIDKENKKLSLSLKKLL-------PDPwENVEEKYPvG 563

                          330       340       350       360       370       380
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517972  730 MLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:PRK00087   564 SIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIK 632
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 179-671 4.10e-19

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 93.31  E-value: 4.10e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  179 LSAEALKPGMLLTGTVSSLEDHGYLVDIG--VDGtraFLPLlkaqEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLS 256
Cdd:PRK06299    23 LKESETREGSIVKGTVVAIDKDYVLVDVGlkSEG---RIPL----EEFKNEQGELEVKVGDEVEVYVERIEDGFGETVLS 95

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  257 VghsevstAIATEQQSWN-LNNLL-PGLVVKAQVQKVTPFGLT--LNfltfftGVVDFM---HLD--PKKAGTYFSNQAV 327
Cdd:PRK06299    96 R-------EKAKRLEAWDkLEKAFeNGEIVEGVINGKVKGGFTvdLN------GVEAFLpgsQVDvrPVRDTDPLEGKEL 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  328 RACILCVHPRTRVVHLSLRPIF--------------LQPGrpltrlscqnlgavldDVpVQGFFKKA---GATFRLK--D 388
Cdd:PRK06299   163 EFKVIKLDKKRNNIVVSRRAVLeeeraeereellenLEEG----------------QV-VEGVVKNItdyGAFVDLGgvD 225

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  389 GVLAYARLSHlsdsKNVFNP-EAFKPGNTHKCRIIDYSQmdELALLSLrtSI----------IEAQYlryhdiEPGAVVK 457
Cdd:PRK06299   226 GLLHITDISW----KRVNHPsEVVNVGDEVKVKVLKFDK--EKKRVSL--GLkqlgedpweaIEKKY------PVGSKVK 291

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  458 GTVLTIKSYGMLVKVGEQMRGLVppmHLADI----LMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTL------IE 527
Cdd:PRK06299   292 GKVTNITDYGAFVELEEGIEGLV---HVSEMswtkKNKHPSKVVSVGQEVEVMVLEIDEEKRRISLGLKQCKenpweeFA 368

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  528 SKLPVitcyadakpGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELS-TEYIPDPERVFYTGQVVKVVVLNCEPSKERM 606
Cdd:PRK06299   369 EKYPV---------GDVVEGKVKNITDFGAFVGLEGGIDGLVHLSDISwDKKGEEAVELYKKGDEVEAVVLKVDVEKERI 439

                          490       500       510       520       530       540
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462517972  607 LLSFK-LSSDPepkkepAGHSQKKGKainIGQLVDVKVLEKTKDGLEVAvLPHNIRAFLPTSHLSD 671
Cdd:PRK06299   440 SLGIKqLEEDP------FEEFAKKHK---KGSIVTGTVTEVKDKGAFVE-LEDGVEGLIRASELSR 495
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 567-798 1.83e-18

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 88.95  E-value: 1.83e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  567 GLVPKHELSTEyipdPERVFYT-GQVVKVVVLNCEPSKERMLLSfklssdpepkKEPAGhsQKKG-----KAINIGQLVD 640
Cdd:COG0539     44 GIIPLSEFSDE----PGELEVKvGDEVEVYVEKVEDGEGEIVLS----------KKKAD--REKAweeleEAFENGEPVE 107

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  641 VKVLEKTKDGLEVAVlpHNIRAFLPTSHLSDH-VAN-GPLLHHWLQAgdilhRVLCLSQSEGRVLLCRKPALVSTVEGGQ 718
Cdd:COG0539    108 GKVKGVVKGGLIVDI--GGVRAFLPASQVDVRpVRDlDEYVGKTLEF-----KIIKLDRKRNNVVVSRRAVLEEEREEKR 180

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  719 DpKNFSEIHPGMLLIGFVKSIKDYGVFIQFPsGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:COG0539    181 E-ELLEKLEEGDVVEGTVKNITDFGAFVDLG-GVDGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKIDREKERISLSLK 258
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 565-798 1.99e-18

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 89.55  E-value: 1.99e-18
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  565 VQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFKLSsdpepkKEPAGHSQKKGKAINiGQLVDVKVL 644
Cdd:PRK06676    42 VEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRL------EAEKAWDKLEEKFEE-GEVVEVKVT 114

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  645 EKTKDGLEVAVlpHNIRAFLPTSHLSDH-VANgpllHHWLQAGDILHRVLCLSQSEGRVLLCRKpALVSTVEGGQDPKNF 723
Cdd:PRK06676   115 EVVKGGLVVDV--EGVRGFIPASLISTRfVED----FSDFKGKTLEVKIIELDPEKNRVILSRR-AVVEEERAAKKEELL 187

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517972  724 SEIHPGMLLIGFVKSIKDYGVFIQFpSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:PRK06676   188 SSLKEGDVVEGTVARLTDFGAFVDI-GGVDGLVHISELSHERVEKPSEVVSVGQEVEVKVLSIDWETERISLSLK 261
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1601-1861 6.96e-17

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 82.85  E-value: 6.96e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1601 RQPESA-DDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKtisfREEQEKLnvwvALLNLENMYGSQESLT 1679
Cdd:COG2956     22 GQPDKAiDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE----RDPDRAE----ALLELAQDYLKAGLLD 93

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1680 K---VFERAVQYNEP-LKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALEC 1755
Cdd:COG2956     94 RaeeLLEKLLELDPDdAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCELAELYLEQGDYDEAIEALEKALKL 173

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1756 LPskEHVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVihLSLAPKRMKFF 1835
Cdd:COG2956    174 DP--DCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAELYEKLGDPEEALELLRKA--LELDPSDDLLL 249

                          250       260
                   ....*....|....*....|....*.
gi 2462517972 1836 FKRYLdYEKQHGTEKdVQAVKAKALE 1861
Cdd:COG2956    250 ALADL-LERKEGLEA-ALALLERQLR 273
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
451-522 4.47e-16

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 74.56  E-value: 4.47e-16
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517972   451 EPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLK 522
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 405-621 8.23e-16

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 81.46  E-value: 8.23e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  405 VFNPEAFKpGNTHKCRIIDYSQMDELALLSlRTSIIEAQYLRYHD-----IEPGAVVKGTVLTIKSYGMLVKVGEqMRGL 479
Cdd:PRK06676   142 VEDFSDFK-GKTLEVKIIELDPEKNRVILS-RRAVVEEERAAKKEellssLKEGDVVEGTVARLTDFGAFVDIGG-VDGL 218

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  480 VppmHLADI---LMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTL------IESKLPVitcyadakpGLQTHGFII 550
Cdd:PRK06676   219 V---HISELsheRVEKPSEVVSVGQEVEVKVLSIDWETERISLSLKDTLpgpwegVEEKLPE---------GDVIEGTVK 286

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517972  551 RVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFKlSSDPEPKKE 621
Cdd:PRK06676   287 RLTDFGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIK-ALEEAPAEE 356
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 729-798 9.35e-16

S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 73.41  E-value: 9.35e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  729 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:cd05698      1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 566-1094 2.52e-15

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 81.32  E-value: 2.52e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  566 QGLVPKHElsteyIPDPERVFYTGQVVKVVVLNCEPSKERMLLSfklssdpepkKEPAGHSQKKGK---AINIGQLVDVK 642
Cdd:TIGR00717   43 EGRIPKEE-----FLDAPLEIQVGDEVEVYLDRVEDRFGETVLS----------REKAQRHELWIKlekAYEEGSIVEGK 107

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  643 VLEKTKDGLEVAVlpHNIRAFLPTSHLSDHVANGPLLHhwlQAGDILHRVLCLSQSEGRVLLCRKPALVSTVEGGQDpKN 722
Cdd:TIGR00717  108 IVGKVKGGFIVDL--NGVEAFLPGSQVDVKPIKDLDSL---IGKTLKFKIIKLDQKRNNIVVSRRAYLEEERSQARE-EL 181

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  723 FSEIHPGMLLIGFVKSIKDYGVFIQFpSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLRLSDc 802
Cdd:TIGR00717  182 LENLKEGDVVKGVVKNITDFGAFVDL-GGVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQLG- 259

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  803 glGD--LAItsllllnqclEELQGVRSLMSNRdsvliqtLAEMTP-GMFLDLV--------VQEVLEDGSVVfsggpvpd 871
Cdd:TIGR00717  260 --EDpwEAI----------EKKFPVGDKITGR-------VTNLTDyGVFVEIEegieglvhVSEMSWVKKNS-------- 312

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  872 lvlKASRYHRAGQEVEsgqkkkVVILNVDLLKLEVHVSLHQDLVN---RKARKLRKGSEHQAIVQHLEKSFAIASLVE-- 946
Cdd:TIGR00717  313 ---HPSKVVKKGDEVE------VMILDIDPERRRLSLGLKQCKANpweQFEEKHPVGDRVTGKIKKITDFGAFVELEGgi 383

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  947 TGHLaafsltsHLNDTFRFDSEKlqvgqgVSLTLKTTEPGVTGLLLAVEGPAAKRTMRPTQKDSETVDEDEEVDPaltvg 1026
Cdd:TIGR00717  384 DGLI-------HLSDISWDKDGR------EADHLYKKGDEIEAVVLAVDKEKKRISLGVKQLTENPWEKFAAKYK----- 445

                          490       500       510       520       530       540
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462517972 1027 tikkhtlsIGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIG 1094
Cdd:TIGR00717  446 --------VGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELSENRDE--DKTDEIKVGDEVEAKVVD 503
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 527-610 3.03e-15

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 72.62  E-value: 3.03e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  527 ESKLPviTCYADAKPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERM 606
Cdd:cd04461      2 EGTLP--TNFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRF 79


                   ....
gi 2462517972  607 LLSF 610
Cdd:cd04461     80 LLSL 83
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
728-798 3.46e-15

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 71.87  E-value: 3.46e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517972   728 PGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
540-611 5.43e-15

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 71.48  E-value: 5.43e-15
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517972   540 KPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFK 611
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 631-1094 7.64e-15

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 79.82  E-value: 7.64e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  631 KAINIGQLVDVKVLEKTKDGLEVAVlpHNIRAFLPTSHLS-----DHvanGPLLHHWLQAgdilhRVLCLSQSEGRVLLC 705
Cdd:PRK06299   110 KAFENGEIVEGVINGKVKGGFTVDL--NGVEAFLPGSQVDvrpvrDT---DPLEGKELEF-----KVIKLDKKRNNIVVS 179

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  706 RKpALVSTVEGGQDPKNFSEIHPGMLLIGFVKSIKDYGVFIQFpSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTN 785
Cdd:PRK06299   180 RR-AVLEEERAEEREELLENLEEGQVVEGVVKNITDYGAFVDL-GGVDGLLHITDISWKRVNHPSEVVNVGDEVKVKVLK 257

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  786 VDEEKQRMLLSLRLsdcgLGD---LAITsllllnqclEELQgVRSLMSNRDSVLiqtlaemTP-GMFLDlvvqevLEDGs 861
Cdd:PRK06299   258 FDKEKKRVSLGLKQ----LGEdpwEAIE---------KKYP-VGSKVKGKVTNI-------TDyGAFVE------LEEG- 309

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  862 vvfsggpVPDLV-----------LKASRYHRAGQEVEsgqkkkVVILNVDLLKLEVHVSLHQDLVN---RKARKLRKGSE 927
Cdd:PRK06299   310 -------IEGLVhvsemswtkknKHPSKVVSVGQEVE------VMVLEIDEEKRRISLGLKQCKENpweEFAEKYPVGDV 376

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  928 HQAivqhleksfAIASLVETGhlaAFsltshlndtfrfdseklqvgqgVSLtlkttEPGVTGLL----LA--VEGPAAKR 1001
Cdd:PRK06299   377 VEG---------KVKNITDFG---AF----------------------VGL-----EGGIDGLVhlsdISwdKKGEEAVE 417

                          410       420       430       440       450       460       470       480
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1002 TMRptqKDSE------TVDEDEE----------VDPALTVgtIKKHTlsIGDMVTGTVKSIKPTHVVVTLEDGIIGCIHA 1065
Cdd:PRK06299   418 LYK---KGDEveavvlKVDVEKErislgikqleEDPFEEF--AKKHK--KGSIVTGTVTEVKDKGAFVELEDGVEGLIRA 490

                          490       500
                   ....*....|....*....|....*....
gi 2462517972 1066 SHILDDvpEGTSPTTKLKVGKTVTARVIG 1094
Cdd:PRK06299   491 SELSRD--RVEDATEVLKVGDEVEAKVIN 517
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1629-1861 3.97e-14

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 74.77  E-value: 3.97e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1629 FHLQATEIEKARAVAERALKtisfrEEQEKLNVWVALLNLENMYGSQESLTKVFERAVQYNEP-LKVFLHLADIYAKSEK 1707
Cdd:COG2956     17 NYLLNGQPDKAIDLLEEALE-----LDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLERDPDrAEALLELAQDYLKAGL 91

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1708 FQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPSKEHVDVIAkfAQLEFQLGDAERAKAIFEN 1787
Cdd:COG2956     92 LDRAEELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLGPENAHAYCEL--AELYLEQGDYDEAIEALEK 169

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517972 1788 TLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVihLSLAPKRMKFFFKRYLDYEKQHGTEKDVQAVKaKALE 1861
Cdd:COG2956    170 ALKLDPDCARALLLLAELYLEQGDYEEAIAALERA--LEQDPDYLPALPRLAELYEKLGDPEEALELLR-KALE 240
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1577-1792 7.98e-13

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 70.91  E-value: 7.98e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1577 ERELEKQKAEKELSRIeeaLMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKtisfrEEQ 1656
Cdd:COG2956     70 ERDPDRAEALLELAQD---YLKAGLLDRAEELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLK-----LGP 141

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1657 EKLNVWVALLNLENMYGSQESLTKVFERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAF 1735
Cdd:COG2956    142 ENAHAYCELAELYLEQGDYDEAIEALEKALKLDpDCARALLLLAELYLEQGDYEEAIAALERALEQDPDYLPALPRLAEL 221

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2462517972 1736 LLRRSQAAASHRVLQRALECLPSkehVDVIAKFAQLEFQLGDAERAKAIFENTLSTY 1792
Cdd:COG2956    222 YEKLGDPEEALELLRKALELDPS---DDLLLALADLLERKEGLEAALALLERQLRRH 275
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 732-796 9.71e-13

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 64.71  E-value: 9.71e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517972  732 LIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLS 796
Cdd:cd00164      1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 449-798 1.06e-12

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 72.22  E-value: 1.06e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  449 DIEPGAVVKGTVLTIKSYGMLVKV-GEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTLIE 527
Cdd:PRK06676    14 EVEVGDVVTGEVLKVEDKQVFVNIeGYKVEGVIPISELSNDHIEDINDVVKVGDELEVYVLKVEDGEGNLLLSKRRLEAE 93

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  528 ---SKLpvITCYADAKPglqthgFIIRVKDY---GCIVKFyNNVQGLVPKHELSTEYIPDPERvfYTGQVVKVVVLNCEP 601
Cdd:PRK06676    94 kawDKL--EEKFEEGEV------VEVKVTEVvkgGLVVDV-EGVRGFIPASLISTRFVEDFSD--FKGKTLEVKIIELDP 162

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  602 SKERMLLSFK--LSSDPEPKKEPAGHSqkkgkaINIGQLVDVKVLEKTK----------DGLevavlphnirafLPTSHL 669
Cdd:PRK06676   163 EKNRVILSRRavVEEERAAKKEELLSS------LKEGDVVEGTVARLTDfgafvdiggvDGL------------VHISEL 224

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  670 S-DHVANgpllhhwlqAGDILH-------RVLCLSQSEGRVLLCRKPALVSTVEGGQDpknfsEIHPGMLLIGFVKSIKD 741
Cdd:PRK06676   225 ShERVEK---------PSEVVSvgqevevKVLSIDWETERISLSLKDTLPGPWEGVEE-----KLPEGDVIEGTVKRLTD 290

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2462517972  742 YGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:PRK06676   291 FGAFVEVLPGVEGLVHISQISHKHIATPSEVLEEGQEVKVKVLEVNEEEKRISLSIK 347
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 456-520 1.14e-12

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 64.71  E-value: 1.14e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517972  456 VKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMT 520
Cdd:cd00164      1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 450-798 7.88e-12

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 70.15  E-value: 7.88e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  450 IEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPpmhLADILmkNPEKKYHIGDEVKCRVLLCDP-EAKKLMMTLKKTLIES 528
Cdd:TIGR00717   16 TRPGSIVKGTVVAINKDTVFVDVGLKSEGRIP---KEEFL--DAPLEIQVGDEVEVYLDRVEDrFGETVLSREKAQRHEL 90

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  529 KLPVITCYADAKPglqTHGFIIRVKDYGCIVKFyNNVQGLVPKHELSTEYIPDPERvfYTGQVVKVVVLNCEPSKERMLL 608
Cdd:TIGR00717   91 WIKLEKAYEEGSI---VEGKIVGKVKGGFIVDL-NGVEAFLPGSQVDVKPIKDLDS--LIGKTLKFKIIKLDQKRNNIVV 164

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  609 SFKLSSDPEPKKEpaghSQKKGKAINIGQLVDVKVLEKTKDGleVAVLPHNIRAFLPTSHLS-DHVANgPllHHWLQAGD 687
Cdd:TIGR00717  165 SRRAYLEEERSQA----REELLENLKEGDVVKGVVKNITDFG--AFVDLGGVDGLLHITDMSwKRVKH-P--SEYVKVGQ 235

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  688 ILH-RVLCLSQSEGRVLLCRKpalvstvEGGQDP-KNFSEIHP-GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMS-D 763
Cdd:TIGR00717  236 EVKvKVIKFDKEKGRISLSLK-------QLGEDPwEAIEKKFPvGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEMSwV 308

                          330       340       350
                   ....*....|....*....|....*....|....*
gi 2462517972  764 KFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:TIGR00717  309 KKNSHPSKVVKKGDEVEVMILDIDPERRRLSLGLK 343
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 1680-1794 8.05e-12

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 64.44  E-value: 8.05e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1680 KVFERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPs 1758
Cdd:COG4783     25 ALLEKALELDpDNPEAFALLGEILLQLGDLDEAIVLLHEALELDPDEPEARLNLGLALLKAGDYDEALALLEKALKLDP- 103

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 2462517972 1759 kEHVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPK 1794
Cdd:COG4783    104 -EHPEAYLRLARAYRALGRPDEAIAALEKALELDPD 138
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 546-609 9.93e-12

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 62.01  E-value: 9.93e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517972  546 HGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLS 609
Cdd:cd00164      2 TGKVVSITKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1035-1094 8.62e-11

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 59.54  E-value: 8.62e-11
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  1035 IGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIG 1094
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVK--DPEEVLKVGDEVKVKVLS 59
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 729-798 1.18e-10

S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 58.84  E-value: 1.18e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  729 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKqRMLLSLR 798
Cdd:cd05692      1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARG-RISLSIK 69
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 727-800 1.76e-10

S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 58.88  E-value: 1.76e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517972  727 HPGMLLIGFVKSIKDYGVFIQF-PSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLRLS 800
Cdd:cd05708      1 KVGQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS 75
rpsA PRK13806
30S ribosomal protein S1; Provisional
 401-687 2.08e-10

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 65.52  E-value: 2.08e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  401 DSKNVFNPEAFKpGNTHKCRIIDYSQ------MDELALLSLRTSIIEAQYLRyhDIEPGAVVKGTVLTIKSYGMLVKVGE 474
Cdd:PRK13806   148 DLRYVEDPESYV-GQTFQFLITRVEEngrnivVSRRALLEREQKEALEAFME--TVKEGDVVEGTVTRLAPFGAFVELAP 224

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  475 QMRGLVppmHLADI---LMKNPEKKYHIGDEVKCRVLLCDPEAK----KLMMTLKKTlieSKLPVITCYADAKPGLQTHG 547
Cdd:PRK13806   225 GVEGMV---HISELswsRVQKADEAVSVGDTVRVKVLGIERAKKgkglRISLSIKQA---GGDPWDTVGDRLKAGDKVTG 298

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  548 FIIRVKDYGCIVKFYNNVQGLVPKHELS-TEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFKlssdpEPKKEP-AGH 625
Cdd:PRK13806   299 KVVRLAPFGAFVEILPGIEGLVHVSEMSwTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLR-----DAEGDPwADV 373

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517972  626 SQKkgkaINIGQLVDVKVLEKTKDGLEVAVLPhNIRAFLPTSHLSDhvANGPLLHHWLQAGD 687
Cdd:PRK13806   374 AER----FAPGTTVTGTVEKRAQFGLFVNLAP-GVTGLLPASVISR--AGKPATYEKLKPGD 428
rpsA PRK13806
30S ribosomal protein S1; Provisional
 537-796 4.93e-10

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 64.36  E-value: 4.93e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  537 ADAKPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKE----RMLLSFK- 611
Cdd:PRK13806   198 ETVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKgkglRISLSIKq 277

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  612 LSSDPepkkepaghSQKKGKAINIGQLVDVKVLEKTKDGLEVAVLPhNIRAFLPTSHLSdHV--ANGPllHHWLQAGDIL 689
Cdd:PRK13806   278 AGGDP---------WDTVGDRLKAGDKVTGKVVRLAPFGAFVEILP-GIEGLVHVSEMS-WTrrVNKP--EDVVAPGDAV 344

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  690 H-RVLCLSQSEGRVLLCRKPAlvstvEGgqDP-KNFSE-IHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFV 766
Cdd:PRK13806   345 AvKIKDIDPAKRRISLSLRDA-----EG--DPwADVAErFAPGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGK 417

                          250       260       270
                   ....*....|....*....|....*....|
gi 2462517972  767 TSTSDHFVEGQTVAAKVTNVDEEKQRMLLS 796
Cdd:PRK13806   418 PATYEKLKPGDSVTLVVEEIDTAKRKISLA 447
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 547-609 1.01e-09

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 56.53  E-value: 1.01e-09
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462517972  547 GFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLS 609
Cdd:pfam00575    9 GEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILS 71
S1_Rrp5_repeat_hs6_sc5 cd05698
S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 453-522 1.05e-09

S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240203 [Multi-domain]  Cd Length: 70  Bit Score: 56.08  E-value: 1.05e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  453 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLK 522
Cdd:cd05698      1 GLKTHGTIVKVKPNGCIVSFYNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPEQQRLLLSCK 70
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 1682-1801 1.46e-09

Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443378 [Multi-domain]  Cd Length: 131  Bit Score: 57.71  E-value: 1.46e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1682 FERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPskE 1760
Cdd:COG4235      6 LRQALAANpNDAEGWLLLGRAYLRLGRYDEALAAYEKALRLDPDNADALLDLAEALLAAGDTEEAEELLERALALDP--D 83

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|.
gi 2462517972 1761 HVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPKRTDVWSV 1801
Cdd:COG4235     84 NPEALYLLGLAAFQQGDYAEAIAAWQKLLALLPADAPARLL 124
PRK08059 PRK08059
general stress protein 13; Validated
 450-524 1.61e-09

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 57.36  E-value: 1.61e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517972  450 IEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKT 524
Cdd:PRK08059     5 YEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRAT 79
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 453-798 1.64e-09

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 61.60  E-value: 1.64e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  453 GAVVKGTVL-TIKSyGMLVKVGEqMRGLVPPMHLADILMKNPEKkyHIGDEVKCRVLLCDPEAKKL-----------MMT 520
Cdd:COG0539    103 GEPVEGKVKgVVKG-GLIVDIGG-VRAFLPASQVDVRPVRDLDE--YVGKTLEFKIIKLDRKRNNVvvsrravleeeREE 178

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  521 LKKTLIEsKLpvitcyadaKPGLQTHGFIIRVKDYGCIVKFyNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCE 600
Cdd:COG0539    179 KREELLE-KL---------EEGDVVEGTVKNITDFGAFVDL-GGVDGLLHISEISWGRVKHPSEVLKVGDEVEVKVLKID 247

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  601 PSKERMLLSFK-LSSDPepkkepaghsqkkgkainigqlvdvkvlektkdglevavlphniraflptshlsdhvangpll 679
Cdd:COG0539    248 REKERISLSLKqLQPDP--------------------------------------------------------------- 264

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  680 hhWLQAGDilhrvlclsqsegrvllcrkpalvstveggqdpknfsEIHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKA 759
Cdd:COG0539    265 --WENIAE-------------------------------------KYPVGDVVKGKVTRLTDFGAFVELEPGVEGLVHIS 305

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|
gi 2462517972  760 IMS-DKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:COG0539    306 EMSwTKRVAHPSDVVKVGDEVEVKVLDIDPEERRISLSIK 345
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 1690-1826 2.08e-09

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 57.51  E-value: 2.08e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1690 EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPskEHVDVIAKFA 1769
Cdd:COG4783      2 ACAEALYALAQALLLAGDYDEAEALLEKALELDPDNPEAFALLGEILLQLGDLDEAIVLLHEALELDP--DEPEARLNLG 79

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2462517972 1770 QLEFQLGDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVIHLS 1826
Cdd:COG4783     80 LALLKAGDYDEALALLEKALKLDPEHPEAYLRLARAYRALGRPDEAIAALEKALELD 136
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
453-527 7.55e-09

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 60.73  E-value: 7.55e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517972  453 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTLIE 527
Cdd:PRK00087   563 GSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEVEEE 637
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 37-346 8.56e-09

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 60.13  E-value: 8.56e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972   37 TEEGSTKRKKSQKGPAKTKKLKIEKRESSKSAREKFEilsvESLCEGMRILGCVKEVNELELVISLPNGLQGFVQVTEIc 116
Cdd:TIGR00717  231 VKVGQEVKVKVIKFDKEKGRISLSLKQLGEDPWEAIE----KKFPVGDKITGRVTNLTDYGVFVEIEEGIEGLVHVSEM- 305

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  117 dAYTKKLNeqvtqeqplkdllHLPELFSPGMLVRCVVssLGItDRGKKSVKLSLNPKNVNRVLSAEALKP-GMLLTGTVS 195
Cdd:TIGR00717  306 -SWVKKNS-------------HPSKVVKKGDEVEVMI--LDI-DPERRRLSLGLKQCKANPWEQFEEKHPvGDRVTGKIK 368

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  196 SLEDHGYLVDIGvDGTRAFLPLLKAQEYIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSVGHsevstaiATEQQSWNL 275
Cdd:TIGR00717  369 KITDFGAFVELE-GGIDGLIHLSDISWDKDGREADHLYKKGDEIEAVVLAVDKEKKRISLGVKQ-------LTENPWEKF 440

                          250       260       270       280       290       300       310
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462517972  276 NNLLP-GLVVKAQVQKVTPFGLTLNFLTFFTGVVDFMHL----DPKKAGTYFSNQAVRACILCVHPRTRVVHLSLR 346
Cdd:TIGR00717  441 AAKYKvGSVVKGKVTEIKDFGAFVELPGGVEGLIRNSELsenrDEDKTDEIKVGDEVEAKVVDIDKKNRKVSLSVK 516
rpsA PRK06299
30S ribosomal protein S1; Reviewed
 182-553 1.15e-08

30S ribosomal protein S1; Reviewed


Pssm-ID: 235775 [Multi-domain]  Cd Length: 565  Bit Score: 59.79  E-value: 1.15e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  182 EALKPGMLLTGTVSSLEDHGYLVDI-GVDGtraflpLLKAQE--YIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSVG 258
Cdd:PRK06299   197 ENLEEGQVVEGVVKNITDYGAFVDLgGVDG------LLHITDisWKRVNHPSEVVNVGDEVKVKVLKFDKEKKRVSLGLK 270

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  259 hsevstaiATEQQSW-NLNNLLP-GLVVKAQVQKVTPFGLtlnFLTFFTGVVDFMHL-------DPKKAGTYFS-NQAVR 328
Cdd:PRK06299   271 --------QLGEDPWeAIEKKYPvGSKVKGKVTNITDYGA---FVELEEGIEGLVHVsemswtkKNKHPSKVVSvGQEVE 339

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  329 ACILCVHPRTRVVHLSLRPifLQPgRPLTRLSCQ-NLGAVlddvpVQGFFK---KAGATFRLKDGVLAYARLSHLSDSKN 404
Cdd:PRK06299   340 VMVLEIDEEKRRISLGLKQ--CKE-NPWEEFAEKyPVGDV-----VEGKVKnitDFGAFVGLEGGIDGLVHLSDISWDKK 411

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  405 VFNP-EAFKPGNTHKCRIIDYSQMDELALLSLR------TSIIEAQYlryhdiEPGAVVKGTVLTIKSYGMLVKVGEQMR 477
Cdd:PRK06299   412 GEEAvELYKKGDEVEAVVLKVDVEKERISLGIKqleedpFEEFAKKH------KKGSIVTGTVTEVKDKGAFVELEDGVE 485

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462517972  478 GLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTLIESKLPVITCYADAKPGLQTHGFIIRVK 553
Cdd:PRK06299   486 GLIRASELSRDRVEDATEVLKVGDEVEAKVINIDRKNRRISLSIKALDEAEEKEAIAEYNSASDSKTTLGDLLKAA 561
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 381-611 1.24e-08

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 60.11  E-value: 1.24e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  381 GATFRLKDGVLAYARLSHLSDSKNVFNP-EAFKPGNTHKCRIIDYSQMDELALLSLRTSI------IEAQYlryhdiEPG 453
Cdd:PRK12269   593 GAFIELAEGIEGLAHISEFSWVKKTSKPsDMVKIGDEVECMILGYDIQAGRVSLGLKQVTanpweeIEARY------PVG 666

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  454 AVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNP-EKKYHIGDEVKCRVLLCDPEAKKLMMTLKKtLIESKLPV 532
Cdd:PRK12269   667 ARFTRRIVKVTNAGAFIEMEEGIDGFLHVDDLSWVKRTRPaDHELEVGKEIECMVIECDPQARRIRLGVKQ-LSDNPWQV 745

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  533 itcYADA-KPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPE---RVFYTGQVVKVVVLNCEPSKERMLL 608
Cdd:PRK12269   746 ---FANAyGVGSTVEGEVSSVTDFGIFVRVPGGVEGLVRKQHLVENRDGDPGealRKYAVGDRVKAVIVDMNVKDRKVAF 822


                   ...
gi 2462517972  609 SFK 611
Cdd:PRK12269   823 SVR 825
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1039-1101 1.35e-08

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 53.15  E-value: 1.35e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462517972 1039 VTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIGGRDMKTF 1101
Cdd:cd00164      1 VTGKVVSITKFGVFVELEDGVEGLVHISELSDKFVK--DPSEVFKVGDEVEVKVLEVDPEKGR 61
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1228-1298 1.98e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 52.61  E-value: 1.98e-08
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462517972  1228 EEGEVAMGRVVKVTPNeGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFVPQKVVRCYILS--TADNVLTLSLR 1298
Cdd:smart00316    1 EVGDVVEGTVTEITPG-GAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSvdEEKGRIILSLK 72
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1322-1395 4.32e-08

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 51.84  E-value: 4.32e-08
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517972  1322 KEGQLLRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQHSPSKKalyNKHLPEGKLLTARVLRLNHQKNLVELSF 1395
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDP---EEVLKVGDEVKVKVLSVDEEKGRIILSL 71
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
1664-1821 4.45e-08

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 56.17  E-value: 4.45e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1664 ALLNLENMYGSQESLTK---VFERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRR 1739
Cdd:COG0457     10 AYNNLGLAYRRLGRYEEaieDYEKALELDpDDAEALYNLGLAYLRLGRYEEALADYEQALELDPDDAEALNNLGLALQAL 89

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1740 SQAAASHRVLQRALECLPskEHVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIF 1819
Cdd:COG0457     90 GRYEEALEDYDKALELDP--DDAEALYNLGLALLELGRYDEAIEAYERALELDPDDADALYNLGIALEKLGRYEEALELL 167


                   ..
gi 2462517972 1820 ER 1821
Cdd:COG0457    168 EK 169
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1327-1394 7.00e-08

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 50.84  E-value: 7.00e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462517972 1327 LRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQhspSKKALYNKHLPEGKLLTARVLRLNHQKNLVELS 1394
Cdd:cd00164      1 VTGKVVSITKFGVFVELEDGVEGLVHISELSD---KFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 729-795 8.51e-08

S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240195 [Multi-domain]  Cd Length: 69  Bit Score: 50.96  E-value: 8.51e-08
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462517972  729 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMS-DKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLL 795
Cdd:cd05690      1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
rpsA TIGR00717
ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found ...
 1030-1394 1.32e-07

ribosomal protein S1; This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification]


Pssm-ID: 273232 [Multi-domain]  Cd Length: 516  Bit Score: 56.28  E-value: 1.32e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1030 KHTLSIGDMVTGTVKSIKPTHVVVTLeDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIGGRDMKTFKYLPISHp 1109
Cdd:TIGR00717  182 LENLKEGDVVKGVVKNITDFGAFVDL-GGVDGLLHITDMSWKRVK--HPSEYVKVGQEVKVKVIKFDKEKGRISLSLKQ- 257

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1110 rfvrTIPElsvrpseledghtalnthsvsPMEKI-KQYQAGQTVTCflKKYNVVKKWLEVEIAPDIRGRIPLLLTSLSFK 1188
Cdd:TIGR00717  258 ----LGED---------------------PWEAIeKKFPVGDKITG--RVTNLTDYGVFVEIEEGIEGLVHVSEMSWVKK 310

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1189 VlKHPDKKFRVGQALRATVVGPDSSKTFLCLSL--TGPHKLEE-------GEVAMGRVVKVTpNEGLTVSFPFGKIGTVS 1259
Cdd:TIGR00717  311 N-SHPSKVVKKGDEVEVMILDIDPERRRLSLGLkqCKANPWEQfeekhpvGDRVTGKIKKIT-DFGAFVELEGGIDGLIH 388

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1260 IFHMS-DSYSETPLEDFVPQKVVRCYILStadnvltLSLRSSRTNPETKSKVEDPEINSIQDIKEGQLLRGYVGSIQPHG 1338
Cdd:TIGR00717  389 LSDISwDKDGREADHLYKKGDEIEAVVLA-------VDKEKKRISLGVKQLTENPWEKFAAKYKVGSVVKGKVTEIKDFG 461

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 2462517972 1339 VFFRLGPSVVGLARYSHVSQHSPSKKALynkHLPEGKLLTARVLRLNHQKNLVELS 1394
Cdd:TIGR00717  462 AFVELPGGVEGLIRNSELSENRDEDKTD---EIKVGDEVEAKVVDIDKKNRKVSLS 514
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 451-517 1.32e-07

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 50.36  E-value: 1.32e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462517972  451 EPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKL 517
Cdd:pfam00575    2 EKGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRI 68
rpsA PRK13806
30S ribosomal protein S1; Provisional
 381-609 1.70e-07

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 55.89  E-value: 1.70e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  381 GATFRLKDGVLAYARLSHLSDSKNVFNPEAFKPGNTHKCRIIDYSQMDELALLSLRTSIIEAQYLRYHDI----EPGAVV 456
Cdd:PRK13806   217 GAFVELAPGVEGMVHISELSWSRVQKADEAVSVGDTVRVKVLGIERAKKGKGLRISLSIKQAGGDPWDTVgdrlKAGDKV 296

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  457 KGTVLTIKSYGMLVKVGEQMRGLVppmHLADI----LMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTLIESKLPV 532
Cdd:PRK13806   297 TGKVVRLAPFGAFVEILPGIEGLV---HVSEMswtrRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADV 373

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462517972  533 ITCYAdakPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLS 609
Cdd:PRK13806   374 AERFA---PGTTVTGTVEKRAQFGLFVNLAPGVTGLLPASVISRAGKPATYEKLKPGDSVTLVVEEIDTAKRKISLA 447
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 729-796 1.77e-07

S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.


Pssm-ID: 240190 [Multi-domain]  Cd Length: 68  Bit Score: 49.92  E-value: 1.77e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462517972  729 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLS 796
Cdd:cd05685      1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRISLS 68
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 1701-1793 1.82e-07

Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures];


Pssm-ID: 444034 [Multi-domain]  Cd Length: 155  Bit Score: 52.66  E-value: 1.82e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1701 IYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPskEHVDVIAKFAQLEFQLGDAER 1780
Cdd:COG5010     63 LYNKLGDFEESLALLEQALQLDPNNPELYYNLALLYSRSGDKDEAKEYYEKALALSP--DNPNAYSNLAALLLSLGQDDE 140

                           90
                   ....*....|...
gi 2462517972 1781 AKAIFENTLSTYP 1793
Cdd:COG5010    141 AKAALQRALGTSP 153
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 728-796 2.18e-07

S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 49.55  E-value: 2.18e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517972  728 PGMLLIGFVKSIKDYGVFIQFpSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLS 796
Cdd:cd05688      1 EGDVVEGTVKSITDFGAFVDL-GGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 1698-1862 2.18e-07

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 54.35  E-value: 2.18e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1698 LADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALEclPSKEHVDVIAKFAQLEFQLGD 1777
Cdd:COG2956     14 KGLNYLLNGQPDKAIDLLEEALELDPETVEAHLALGNLYRRRGEYDRAIRIHQKLLE--RDPDRAEALLELAQDYLKAGL 91

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1778 AERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVIHLSlaPKRMKFFFKRYLDYEKQHGTEKDVQAVKa 1857
Cdd:COG2956     92 LDRAEELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEVLERLLKLG--PENAHAYCELAELYLEQGDYDEAIEALE- 168


                   ....*
gi 2462517972 1858 KALEY 1862
Cdd:COG2956    169 KALKL 173
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 729-797 2.70e-07

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 49.59  E-value: 2.70e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517972  729 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSL 797
Cdd:pfam00575    4 GDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVEDPDEVIKVGDEVKVKVLKVDKDRRRIILSI 72
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
1701-1794 3.80e-07

Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 49.78  E-value: 3.80e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1701 IYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRvLQRALECLPskEHVDVIAKFAQLEFQLGDAER 1780
Cdd:COG3063      1 LYLKLGDLEEAEEYYEKALELDPDNADALNNLGLLLLEQGRYDEAIA-LEKALKLDP--NNAEALLNLAELLLELGDYDE 77

                           90
                   ....*....|....
gi 2462517972 1781 AKAIFENTLSTYPK 1794
Cdd:COG3063     78 ALAYLERALELDPS 91
PRK03987 PRK03987
translation initiation factor IF-2 subunit alpha; Validated
 728-798 4.35e-07

translation initiation factor IF-2 subunit alpha; Validated


Pssm-ID: 235188 [Multi-domain]  Cd Length: 262  Bit Score: 53.29  E-value: 4.35e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517972  728 PGMLLIGFVKSIKDYGVFI---QFPsGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:PRK03987     8 EGELVVGTVKEVKDFGAFVtldEYP-GKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSLK 80
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
1594-1783 1.01e-06

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 51.93  E-value: 1.01e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1594 EALMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTisfreeqeKLNVWVALLNLENMYG 1673
Cdd:COG0457     16 LAYRRLGRYEEAIEDYEKALELDPDDAEALYNLGLAYLRLGRYEEALADYEQALEL--------DPDDAEALNNLGLALQ 87

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1674 SQESLTK---VFERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVL 1749
Cdd:COG0457     88 ALGRYEEaleDYDKALELDpDDAEALYNLGLALLELGRYDEAIEAYERALELDPDDADALYNLGIALEKLGRYEEALELL 167

                          170       180       190
                   ....*....|....*....|....*....|....
gi 2462517972 1750 QRALECLPSKEHVDVIAKFAQLEFQLGDAERAKA 1783
Cdd:COG0457    168 EKLEAAALAALLAAALGEAALALAAAEVLLALLL 201
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 1033-1431 1.03e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 53.34  E-value: 1.03e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1033 LSIGDMVTGTVKSIKPTHVVVTLEDGII-GCIHASHILDDVPEGTSPTtkLKVGKTVTARVIGGRDMKtfKYLpishprf 1111
Cdd:PRK06676    15 VEVGDVVTGEVLKVEDKQVFVNIEGYKVeGVIPISELSNDHIEDINDV--VKVGDELEVYVLKVEDGE--GNL------- 83

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1112 vrtipELSVRPSELEDGHTALNthsvspmekiKQYQAGQTVTCFLKKynVVKKWLEVEIApDIRGRIPLLLTSLSFKvlk 1191
Cdd:PRK06676    84 -----LLSKRRLEAEKAWDKLE----------EKFEEGEVVEVKVTE--VVKGGLVVDVE-GVRGFIPASLISTRFV--- 142

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1192 hPDKKFRVGQALRATVVGPDSSKTFLCLSltgpHK-----------------LEEGEVAMGRVVKVTPnegltvsfpFG- 1253
Cdd:PRK06676   143 -EDFSDFKGKTLEVKIIELDPEKNRVILS----RRavveeeraakkeellssLKEGDVVEGTVARLTD---------FGa 208

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1254 --KIGTVS-IFHMSD-SYS--ETPLEDFVPQKVVRCYILStAD---NVLTLSLRSsrTNPETKSKVEdpeinsiQDIKEG 1324
Cdd:PRK06676   209 fvDIGGVDgLVHISElSHErvEKPSEVVSVGQEVEVKVLS-IDwetERISLSLKD--TLPGPWEGVE-------EKLPEG 278

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1325 QLLRGYVGSIQPHGVFFRLGPSVVGLArysHVSQHSpskkalyNKH-------LPEGKLLTARVLRLNHQKNLVELSflp 1397
Cdd:PRK06676   279 DVIEGTVKRLTDFGAFVEVLPGVEGLV---HISQIS-------HKHiatpsevLEEGQEVKVKVLEVNEEEKRISLS--- 345

                          410       420       430
                   ....*....|....*....|....*....|....
gi 2462517972 1398 gdtgKPDVLSASLEGQLTKQEERKTEAEErDQKG 1431
Cdd:PRK06676   346 ----IKALEEAPAEEEDRREEYRQYELPE-EETG 374
PRK08059 PRK08059
general stress protein 13; Validated
 724-798 1.16e-06

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 49.27  E-value: 1.16e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517972  724 SEIHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:PRK08059     3 SQYEVGSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIR 77
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 542-611 1.20e-06

S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 47.67  E-value: 1.20e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  542 GLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPsKERMLLSFK 611
Cdd:cd05692      1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISLSIK 69
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 449-521 1.22e-06

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 47.97  E-value: 1.22e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462517972  449 DIEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTL 521
Cdd:cd04461     11 DLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDEEKQRFLLSL 83
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 1317-1395 1.33e-06

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 47.97  E-value: 1.33e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517972 1317 SIQDIKEGQLLRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQHSPSKKalyNKHLPEGKLLTARVLRLNHQKNLVELSF 1395
Cdd:cd04461      8 NFSDLKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFVTDP---SFGFKKGQSVTAKVTSVDEEKQRFLLSL 83
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
185-256 1.47e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 47.60  E-value: 1.47e-06
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517972   185 KPGMLLTGTVSSLEDHGYLVDIGvDGTRAFLPLLKAQEYiRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLS 256
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVDLG-NGVEGLIPISELSDK-RVKDPEEVLKVGDEVKVKVLSVDEEKGRIILS 70
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 453-522 1.85e-06

S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 47.32  E-value: 1.85e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517972  453 GAVVKGTVLTIKSYGMLVKV-GEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLK 522
Cdd:cd05708      3 GQKIDGTVRRVEDYGVFIDIdGTNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLK 73
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 378-434 2.16e-06

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 46.60  E-value: 2.16e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2462517972  378 KKAGATFRLKDGVLAYARLSHLSDSKNVFNPEAFKPGNTHKCRIIDYSQMDELALLS 434
Cdd:cd00164      9 TKFGVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1_IF2_alpha cd04452
S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. ...
 729-798 2.50e-06

S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to complete the initiation complex, which is competent to begin translation. The IF2a subunit is a major site of control of the translation initiation process, via phosphorylation of a specific serine residue. This alpha subunit is well conserved in eukaryotes and archaea but is not present in bacteria. IF2 is a cold-shock-inducible protein.


Pssm-ID: 239899 [Multi-domain]  Cd Length: 76  Bit Score: 46.81  E-value: 2.50e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462517972  729 GMLLIGFVKSIKDYGVFI---QFPsGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:cd04452      4 GELVVVTVKSIADMGAYVsllEYG-NIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLSKK 75
RNA14 COG5107
Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and ...
 1609-1869 2.96e-06

Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification];


Pssm-ID: 227438 [Multi-domain]  Cd Length: 660  Bit Score: 52.33  E-value: 2.96e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1609 FDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALK---TISFR-EEQEKLNvwvalLNLENMYGSQESLTKVFER 1684
Cdd:COG5107    291 HNQILDYFYYAEEVWFDYSEYLIGISDKQKALKTVERGIEmspSLTMFlSEYYELV-----NDEEAVYGCFDKCTQDLKR 365

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1685 AVQYNEplkvflhlADIYAKSE-KFQEAGELynrMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALEcLPSKEHvD 1763
Cdd:COG5107    366 KYSMGE--------SESASKVDnNFEYSKEL---LLKRINKLTFVFCVHLNYVLRKRGLEAARKLFIKLRK-EGIVGH-H 432

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1764 VIAKFAQLEFQ-LGDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVIHlSLAPKRMKFFFKRYLDY 1842
Cdd:COG5107    433 VYIYCAFIEYYaTGDRATAYNIFELGLLKFPDSTLYKEKYLLFLIRINDEENARALFETSVE-RLEKTQLKRIYDKMIEY 511

                          250       260
                   ....*....|....*....|....*..
gi 2462517972 1843 EKQHGTEKDVQAVKAKALEYVEAKSSV 1869
Cdd:COG5107    512 ESMVGSLNNVYSLEERFRELVPQENLI 538
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 182-524 4.12e-06

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 51.20  E-value: 4.12e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  182 EALKPGMLLTGTVSSLEDHGYLVDIGvdGTRAFLPLlkAQEYIRQKNKGAKLkVGQYLNCIVEKV--KGNGGVVSlsvgH 259
Cdd:COG0539     98 EAFENGEPVEGKVKGVVKGGLIVDIG--GVRAFLPA--SQVDVRPVRDLDEY-VGKTLEFKIIKLdrKRNNVVVS----R 168

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  260 SEVSTAIATEQQSWNLNNLLPGLVVKAQVQKVTPFGLTLNFltfftGVVDFMhldpkkagtyfsnqavracilcvhprtr 339
Cdd:COG0539    169 RAVLEEEREEKREELLEKLEEGDVVEGTVKNITDFGAFVDL-----GGVDGL---------------------------- 215

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  340 vVHLSlrpiflqpgrpltrlscqnlgavlDdvpvqgffkkagatfrlkdgvLAYARLSHLSdsknvfnpEAFKPGNTHKC 419
Cdd:COG0539    216 -LHIS------------------------E---------------------ISWGRVKHPS--------EVLKVGDEVEV 241

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  420 RIIDYSQMDELALLSLRT------SIIEAQYlryhdiEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVppmHLADILM--- 490
Cdd:COG0539    242 KVLKIDREKERISLSLKQlqpdpwENIAEKY------PVGDVVKGKVTRLTDFGAFVELEPGVEGLV---HISEMSWtkr 312

                          330       340       350
                   ....*....|....*....|....*....|....*
gi 2462517972  491 -KNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKT 524
Cdd:COG0539    313 vAHPSDVVKVGDEVEVKVLDIDPEERRISLSIKQL 347
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 454-618 5.67e-06

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 50.57  E-value: 5.67e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  454 AVVKGTVLTIKSYGMLVKVgEQMRGLVPPMHLAdilmKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLKKTLIESKLPVI 533
Cdd:PRK07400   120 ATVRSEVFATNRGGALVRI-EGLRGFIPGSHIS----TRKPKEELVGEELPLKFLEVDEERNRLVLSHRRALVERKMNRL 194

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  534 tcyadaKPGLQTHGFIIRVKDYGCIVKFyNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFKlS 613
Cdd:PRK07400   195 ------EVGEVVVGTVRGIKPYGAFIDI-GGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLSTK-Q 266


                   ....*
gi 2462517972  614 SDPEP 618
Cdd:PRK07400   267 LEPEP 271
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
378-436 5.95e-06

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 45.67  E-value: 5.95e-06
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517972   378 KKAGATFRLKDGVLAYARLSHLSDSKNVFNPEAFKPGNTHKCRIIDYSQMDELALLSLR 436
Cdd:smart00316   14 TPGGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_Rrp5_repeat_hs14 cd05705
S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 726-796 6.68e-06

S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240210 [Multi-domain]  Cd Length: 74  Bit Score: 45.47  E-value: 6.68e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517972  726 IHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTS---DHFVEGQTVAAKVTNVDEEKQRMLLS 796
Cdd:cd05705      1 IKEGQLLRGYVSSVTKQGVFFRLSSSIVGRVLFQNVTKYFVSDPSlynKYLPEGKLLTAKVLSVNSEKNLVELS 74
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 80-170 9.87e-06

S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240209 [Multi-domain]  Cd Length: 72  Bit Score: 45.04  E-value: 9.87e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972   80 LCEGMRILGCVKEVNELE-LVISLPNGLQGFVQVTEICDAYTkklneqvtqEQPLKDllhlpelFSPGMLVRCVVSSlgi 158
Cdd:cd05704      1 LEEGAVTLGMVTKVIPHSgLTVQLPFGKTGLVSIFHLSDSYT---------ENPLEG-------FKPGKIVRCCILS--- 61

                           90
                   ....*....|..
gi 2462517972  159 tdRGKKSVKLSL 170
Cdd:cd05704     62 --KKDGKYQLSL 71
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
1147-1221 1.12e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 44.90  E-value: 1.12e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517972  1147 QAGQTVTCFLKkyNVVKKWLEVEIAPDIRGRIPLllTSLSFKVLKHPDKKFRVGQALRATVVGPDSSKTFLCLSL 1221
Cdd:smart00316    1 EVGDVVEGTVT--EITPGGAFVDLGNGVEGLIPI--SELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 729-796 1.30e-05

S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240212 [Multi-domain]  Cd Length: 68  Bit Score: 44.59  E-value: 1.30e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462517972  729 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLS 796
Cdd:cd05707      1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 626-900 1.58e-05

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 49.49  E-value: 1.58e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  626 SQKKGKAINIGQLVDVKVLEKTKDGLEVAVLPHNIRAFLPTSHLS-DHVANGPLLhhwLQAGDILH-RVLCLSQSEGRVL 703
Cdd:PRK06676     8 SLNSVKEVEVGDVVTGEVLKVEDKQVFVNIEGYKVEGVIPISELSnDHIEDINDV---VKVGDELEvYVLKVEDGEGNLL 84

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  704 LCRKPALVStveggqdpKNFSEI----HPGMLLIGFVKSIKDYGVFIQFpSGLSGLAPKAIMSDKFVTSTSDhFVeGQTV 779
Cdd:PRK06676    85 LSKRRLEAE--------KAWDKLeekfEEGEVVEVKVTEVVKGGLVVDV-EGVRGFIPASLISTRFVEDFSD-FK-GKTL 153

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  780 AAKVTNVDEEKQRMLLSLRlsdcglgdlAItsllllnqcLEElqgvrSLMSNRDSVLiQTLAEmtpGMFLDLVVQEVLED 859
Cdd:PRK06676   154 EVKIIELDPEKNRVILSRR---------AV---------VEE-----ERAAKKEELL-SSLKE---GDVVEGTVARLTDF 206

                          250       260       270       280
                   ....*....|....*....|....*....|....*....|....*
gi 2462517972  860 GSVVFSGGpVPDLV----LKASRYHRAGQEVESGQKKKVVILNVD 900
Cdd:PRK06676   207 GAFVDIGG-VDGLVhiseLSHERVEKPSEVVSVGQEVEVKVLSID 250
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1234-1297 1.96e-05

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 43.91  E-value: 1.96e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517972 1234 MGRVVKVTPNeGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFVPQKVVRCYILSTADNVLTLSL 1297
Cdd:cd00164      2 TGKVVSITKF-GVFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISL 64
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
44-346 2.13e-05

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 49.56  E-value: 2.13e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972   44 RKKSQKGPAKTKKLKIEKRESSKSAREKFEilsveslcEGMRILGCVKEVNELELVISLpNGLQGFVQVTEICDAYTKKL 123
Cdd:PRK00087   359 KLEDEDGYVVLSKKEADREKAWKELEEAFE--------NGEPVKGKVKEVVKGGLLVDY-GGVRAFLPASHVELGYVEDL 429

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  124 NEQVTQEQPLKDLLhlpelFSPGMLVRCVVSslgitdrgKKSVKLSLNPKNVNRVLsaEALKPGMLLTGTVSSLEDHGYL 203
Cdd:PRK00087   430 SEYKGQELEVKIIE-----FNRKRRKKVVLS--------RKAILEEEKEKKKEETW--NSLEEGDVVEGEVKRLTDFGAF 494

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  204 VDI-GVDGtraflpLLKAQE--YIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLSvghsevstaiateqqswnLNNLLP 280
Cdd:PRK00087   495 VDIgGVDG------LLHVSEisWGRVEKPSDVLKVGDEIKVYILDIDKENKKLSLS------------------LKKLLP 550

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  281 ------------GLVVKAQVQKVTPFGLtlnFLTFFTGVVDFMHLD---------PKKAgtYFSNQAVRACILCVHPRTR 339
Cdd:PRK00087   551 dpwenveekypvGSIVLGKVVRIAPFGA---FVELEPGVDGLVHISqiswkridkPEDV--LSEGEEVKAKILEVDPEEK 625


                   ....*..
gi 2462517972  340 VVHLSLR 346
Cdd:PRK00087   626 RIRLSIK 632
COG4700 COG4700
Uncharacterized conserved protein ECs_4300, contains TPR-like domain [Function unknown];
1683-1839 2.24e-05

Uncharacterized conserved protein ECs_4300, contains TPR-like domain [Function unknown];


Pssm-ID: 443735 [Multi-domain]  Cd Length: 249  Bit Score: 47.95  E-value: 2.24e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1683 ERAVQYNEPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVwIKYGA----FLLRRSQAAASHrvLQRALECLPS 1758
Cdd:COG4700     80 EKALEFADTVQNRVRLADALLELGRYDEAIELYEEALTGIFADDPH-ILLGLaqalFELGRYAEALET--LEKLIAKNPD 156

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1759 KEHVDVIAKFAQ-LEfQLGDAERAKAIFENTLSTYPKRtDVWSVYIDMTIKHGSQKDVRDIFERVIHLSlapKRMKFFFK 1837
Cdd:COG4700    157 FKSSDAHLLYARaLE-ALGDLEAAEAELEALARRYSGP-EARYRYAKFLARQGRTAEAKELLEEILDEA---KHMPKHYR 231


                   ..
gi 2462517972 1838 RY 1839
Cdd:COG4700    232 RL 233
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
82-170 2.52e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 43.75  E-value: 2.52e-05
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972    82 EGMRILGCVKEVNELELVISLPNGLQGFVQVTEICDAYTKKLNEQvtqeqplkdllhlpelFSPGMLVRCVVSSLgitDR 161
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKDPEEV----------------LKVGDEVKVKVLSV---DE 62


                    ....*....
gi 2462517972   162 GKKSVKLSL 170
Cdd:smart00316   63 EKGRIILSL 71
RpsA COG0539
Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 ...
 1032-1388 3.34e-05

Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]; Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit


Pssm-ID: 440305 [Multi-domain]  Cd Length: 348  Bit Score: 48.12  E-value: 3.34e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1032 TLSIGDMVTGTVKSIKPTHVVVTL---EDGIIgciHASHILDDvpegtSPTTKLKVGKTVTARVIGGRDmktfkylpish 1108
Cdd:COG0539     15 ELKEGDIVKGTVVSIDDDEVLVDIgykSEGII---PLSEFSDE-----PGELEVKVGDEVEVYVEKVED----------- 75

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1109 pRFVRTIpeLSVRPSELEDGhtalnthsvspMEKIKQ-YQAGQTVTCFLKkyNVVKKWLEVEIApDIRGRIP-------- 1179
Cdd:COG0539     76 -GEGEIV--LSKKKADREKA-----------WEELEEaFENGEPVEGKVK--GVVKGGLIVDIG-GVRAFLPasqvdvrp 138

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1180 ------LLLTSLSFKVLKHpDKKFR--VG----------QALRATVVGpdssktflclsltgphKLEEGEVAMGRVVKVT 1241
Cdd:COG0539    139 vrdldeYVGKTLEFKIIKL-DRKRNnvVVsrravleeerEEKREELLE----------------KLEEGDVVEGTVKNIT 201

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1242 pNEGLTVSFPfGKIGTVsifHMSD-SYS--ETPlEDFVpqKV---VRCYILS--TADNVLTLSLrssrtnpetKSKVEDP 1313
Cdd:COG0539    202 -DFGAFVDLG-GVDGLL---HISEiSWGrvKHP-SEVL--KVgdeVEVKVLKidREKERISLSL---------KQLQPDP 264

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517972 1314 EINSIQDIKEGQLLRGYVGSIQPHGVFFRLGPSVVGLArysHVSQHSPSKKalyNKH----LPEGKLLTARVLRLNHQK 1388
Cdd:COG0539    265 WENIAEKYPVGDVVKGKVTRLTDFGAFVELEPGVEGLV---HISEMSWTKR---VAHpsdvVKVGDEVEVKVLDIDPEE 337
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 449-508 3.45e-05

Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 45.17  E-value: 3.45e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462517972  449 DIEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVppmH---LADILMKNPEKKYHIGDEVKCRVL 508
Cdd:COG1098      2 SIEVGDIVEGKVTGITPFGAFVELPEGTTGLV---HiseIADGYVKDINDYLKVGDEVKVKVL 61
PRK11824 PRK11824
polynucleotide phosphorylase/polyadenylase; Provisional
 724-798 5.05e-05

polynucleotide phosphorylase/polyadenylase; Provisional


Pssm-ID: 236995 [Multi-domain]  Cd Length: 693  Bit Score: 48.12  E-value: 5.05e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517972  724 SEIHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDeEKQRMLLSLR 798
Cdd:PRK11824   617 AEPEVGEIYEGKVVRIVDFGAFVEILPGKDGLVHISEIADERVEKVEDVLKEGDEVKVKVLEID-KRGRIRLSRK 690
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
634-707 5.25e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 42.98  E-value: 5.25e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517972   634 NIGQLVDVKVLEKTKDGLEVAvLPHNIRAFLPTSHLSDHvaNGPLLHHWLQAGDILH-RVLCLSQSEGRVLLCRK 707
Cdd:smart00316    1 EVGDVVEGTVTEITPGGAFVD-LGNGVEGLIPISELSDK--RVKDPEEVLKVGDEVKvKVLSVDEEKGRIILSLK 72
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 1036-1093 5.33e-05

S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 43.00  E-value: 5.33e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2462517972 1036 GDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPegTSPTTKLKVGKTVTARVI 1093
Cdd:cd05697      1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRL--KHPEKKFKPGLKVKCRVL 56
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
280-346 5.68e-05

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 42.98  E-value: 5.68e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517972   280 PGLVVKAQVQKVTPFGLTLNFLTFFTGVVDFMHLDPKKAG----TYFSNQAVRACILCVHPRTRVVHLSLR 346
Cdd:smart00316    2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDKRVKdpeeVLKVGDEVKVKVLSVDEEKGRIILSLK 72
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 453-522 5.85e-05

S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240196 [Multi-domain]  Cd Length: 73  Bit Score: 43.03  E-value: 5.85e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  453 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLK 522
Cdd:cd05691      1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIK 70
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 1594-1721 6.15e-05

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 44.80  E-value: 6.15e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1594 EALMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTisFREEQEklnVWVALLNLENMYG 1673
Cdd:COG4783     12 QALLLAGDYDEAEALLEKALELDPDNPEAFALLGEILLQLGDLDEAIVLLHEALEL--DPDEPE---ARLNLGLALLKAG 86

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 2462517972 1674 SQESLTKVFERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKR 1721
Cdd:COG4783     87 DYDEALALLEKALKLDpEHPEAYLRLARAYRALGRPDEAIAALEKALEL 135
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1322-1397 6.94e-05

S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 42.70  E-value: 6.94e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462517972 1322 KEGQLLRGYVGSIQPHGVFFRL-GPSVVGLArysHVSQHSPSKKALYNKHLPEGKLLTARVLRLNHQKNLVELSFLP 1397
Cdd:cd05708      1 KVGQKIDGTVRRVEDYGVFIDIdGTNVSGLC---HKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKA 74
YabR COG1098
Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function ...
 547-629 8.52e-05

Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only];


Pssm-ID: 440715 [Multi-domain]  Cd Length: 130  Bit Score: 44.01  E-value: 8.52e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  547 GFIIRVKDYGCIVKFYNNVQGLVpkH--ELSTEYIPDPERVFYTGQVVKVVVLNCEPSKeRMLLSFK-LSSDPEPKKEPA 623
Cdd:COG1098     11 GKVTGITPFGAFVELPEGTTGLV--HisEIADGYVKDINDYLKVGDEVKVKVLSIDEDG-KISLSIKqAEEKPKRPPRPR 87


                   ....*.
gi 2462517972  624 GHSQKK 629
Cdd:COG1098     88 RNSRPK 93
CpoB COG1729
Cell division protein CpoB, coordinates peptidoglycan biosynthesis and outer membrane ...
 1700-1794 1.01e-04

Cell division protein CpoB, coordinates peptidoglycan biosynthesis and outer membrane constriction [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 441335 [Multi-domain]  Cd Length: 113  Bit Score: 43.44  E-value: 1.01e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1700 DIYAKSEKFQEAGELYNRMLKRFRQEK---AVWIKYGAFLLRRSQAAASHRVLQRALECLP-SKEHVDVIAKFAQLEFQL 1775
Cdd:COG1729      1 KALLKAGDYDEAIAAFKAFLKRYPNSPlapDALYWLGEAYYALGDYDEAAEAFEKLLKRYPdSPKAPDALLKLGLSYLEL 80

                           90
                   ....*....|....*....
gi 2462517972 1776 GDAERAKAIFENTLSTYPK 1794
Cdd:COG1729     81 GDYDKARATLEELIKKYPD 99
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 452-517 1.03e-04

S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 42.23  E-value: 1.03e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517972  452 PGAVVKGTVLTIKSYGMLVKVGeQMRGLVppmHLADIL---MKNPEKKYHIGDEVKCRVLLCDPEAKKL 517
Cdd:cd05688      1 EGDVVEGTVKSITDFGAFVDLG-GVDGLL---HISDMSwgrVKHPSEVVNVGDEVEVKVLKIDKERKRI 65
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 453-508 1.08e-04

S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240207 [Multi-domain]  Cd Length: 70  Bit Score: 42.19  E-value: 1.08e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517972  453 GAVVKGTVLTIKSYGMLVKVGEQMRGLVppmHLADIL-----MKNPEKKYHIGDEVKCRVL 508
Cdd:cd05702      1 GDLVKAKVKSVKPTQLNVQLADNVHGRI---HVSEVFdewpdGKNPLSKFKIGQKIKARVI 58
S1 pfam00575
S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is ...
 1035-1094 1.09e-04

S1 RNA binding domain; The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.


Pssm-ID: 425760 [Multi-domain]  Cd Length: 72  Bit Score: 42.27  E-value: 1.09e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1035 IGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIG 1094
Cdd:pfam00575    3 KGDVVEGEVTRVTKGGAFVDLGNGVEGFIPISELSDDHVE--DPDEVIKVGDEVKVKVLK 60
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 726-801 1.13e-04

S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240198 [Multi-domain]  Cd Length: 100  Bit Score: 42.97  E-value: 1.13e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  726 IHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVT-------------------STSDHFVEGQTVAAKVTNV 786
Cdd:cd05693      1 LSEGMLVLGQVKEITKLDLVISLPNGLTGYVPITNISDAYTErleeldeeseeeddeeelpDLEDLFSVGQLVRCKVVSL 80

                           90
                   ....*....|....*...
gi 2462517972  787 DEE---KQRMLLSLRLSD 801
Cdd:cd05693     81 DKSksgKKRIELSLEPEL 98
PRK08059 PRK08059
general stress protein 13; Validated
 552-629 1.31e-04

general stress protein 13; Validated


Pssm-ID: 181215 [Multi-domain]  Cd Length: 123  Bit Score: 43.50  E-value: 1.31e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517972  552 VKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFKLSSD-PEPKKEPAGHSQKK 629
Cdd:PRK08059    18 IQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIRATEEaPEAKRKKGKILIPN 96
Suf pfam05843
Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of ...
 1728-1870 1.41e-04

Suppressor of forked protein (Suf); This family consists of several eukaryotic suppressor of forked (Suf) like proteins. The Drosophila melanogaster Suppressor of forked [Su(f)] protein shares homology with the yeast RNA14 protein and the 77-kDa subunit of human cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilization and an important role of the GU-rich sequence for this regulation to occur.


Pssm-ID: 428647 [Multi-domain]  Cd Length: 291  Bit Score: 45.83  E-value: 1.41e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1728 VWIKYGAFLlRRSQAAASHR-VLQRALEclpsKEHV--DVIAKFAQLEFQLG-DAERAKAIFENTLSTYPKRTDVWSVYI 1803
Cdd:pfam05843    3 VWIQYMRAM-RRAEGIKGARkVFKKARK----RPRLtyHVYVASALMEYYCSkDPAVAFKIFELGLKLFPEDEEFVLKYL 77

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462517972 1804 DMTIKHGSQKDVRDIFERVIHlSLAPKRM-KFFFKRYLDYEKQHGTEKDVQAVKAKALEYVEAKSSVL 1870
Cdd:pfam05843   78 DYLISLNDDNNARVLFERVLT-RLAQEKEaKPLWKKFISYESTFGDLASILKLEKRMAELFPEDPPLA 144
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 453-517 1.46e-04

S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240195 [Multi-domain]  Cd Length: 69  Bit Score: 41.71  E-value: 1.46e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517972  453 GAVVKGTVLTIKSYGMLVKVGEQMRGLVppmHLADI----LMKNPEKKYHIGDEVKCRVLLCDPEAKKL 517
Cdd:cd05690      1 GTVVSGKIKSITDFGIFVGLDGGIDGLV---HISDIswtqRVRHPSEIYKKGQEVEAVVLNIDVERERI 66
S1_RecJ_like cd04473
S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of ...
 447-507 1.62e-04

S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.


Pssm-ID: 239919 [Multi-domain]  Cd Length: 77  Bit Score: 41.82  E-value: 1.62e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517972  447 YHDIEPGAVVKGTVLTIKSYGMLVKVGEQMRGLvppMHLADILMknpekKYHIGDEVKCRV 507
Cdd:cd04473     11 MEDLEVGKLYKGKVNGVAKYGVFVDLNDHVRGL---IHRSNLLR-----DYEVGDEVIVQV 63
PTZ00121 PTZ00121
MAEBL; Provisional
 1402-1659 1.65e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 47.06  E-value: 1.65e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1402 KPDVLSASLEgQLTKQEERKTEAEERDQKGEKKNQKRNEKKN----QKGQEEVempsKEKQQPQKPQAQKRGGRECRESG 1477
Cdd:PTZ00121  1379 KADAAKKKAE-EKKKADEAKKKAEEDKKKADELKKAAAAKKKadeaKKKAEEK----KKADEAKKKAEEAKKADEAKKKA 1453

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1478 SEQERVSKKPKKAGLSEEDDSLVDvyYREGKEEAEETNVLPKEKQTKPAEAPRLQLSSGFAwnvglDSLTPA-------- 1549
Cdd:PTZ00121  1454 EEAKKAEEAKKKAEEAKKADEAKK--KAEEAKKADEAKKKAEEAKKKADEAKKAAEAKKKA-----DEAKKAeeakkade 1526

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1550 LPPLAESSDSEEDEKPHQ---ATQIKKSKKERELEKQKAEKELSRIEEALMDPGRQPESADDFDRLVLSSPNSSILWLQY 1626
Cdd:PTZ00121  1527 AKKAEEAKKADEAKKAEEkkkADELKKAEELKKAEEKKKAEEAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKK 1606

                          250       260       270
                   ....*....|....*....|....*....|...
gi 2462517972 1627 MAFHlQATEIEKARAVAERALKTISFREEQEKL 1659
Cdd:PTZ00121  1607 MKAE-EAKKAEEAKIKAEELKKAEEEKKKVEQL 1638
S1_Rrp5_repeat_sc12 cd05708
S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 547-613 1.66e-04

S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240213 [Multi-domain]  Cd Length: 77  Bit Score: 41.93  E-value: 1.66e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462517972  547 GFIIRVKDYGCIVKFYN-NVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLSFKLS 613
Cdd:cd05708      8 GTVRRVEDYGVFIDIDGtNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAEKKRISLGLKAS 75
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 453-515 1.76e-04

S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 41.50  E-value: 1.76e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462517972  453 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAK 515
Cdd:cd05692      1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGR 63
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 1036-1094 1.84e-04

S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240196 [Multi-domain]  Cd Length: 73  Bit Score: 41.49  E-value: 1.84e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517972 1036 GDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVIG 1094
Cdd:cd05691      1 GSIVTGKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVE--DATERFKVGDEVEAKITN 57
rpsA PRK13806
30S ribosomal protein S1; Provisional
 446-798 2.24e-04

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 45.87  E-value: 2.24e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  446 RYHDIEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPmhlADILMKNPEKKYHIGDEVKCRVLLCDPEAKKL-------- 517
Cdd:PRK13806    28 RKTELRVGDKITGTVIAITEDSVFVDTGSKVDGVVDR---AELLDADGELTVAVGDEVELYVVSVNGQEIRLskalsgqg 104

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  518 -MMTLKKTLiESKLPVITCYADAKPGlqthGFIIRV--KDYGCivkfynnvqglvPKHELSTEYIPDPERvfYTGQVVKV 594
Cdd:PRK13806   105 gAAMLEEAY-ENGVPVEGKVTGTCKG----GFNVEVlgRRAFC------------PVSQIDLRYVEDPES--YVGQTFQF 165

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  595 VVLNCEPSKERMLLSFKLSSDPEPKKEPAGHSQKkgkaINIGQLVDVKVLEKTKDGLEVAVLPhNIRAFLPTSHLSDHVA 674
Cdd:PRK13806   166 LITRVEENGRNIVVSRRALLEREQKEALEAFMET----VKEGDVVEGTVTRLAPFGAFVELAP-GVEGMVHISELSWSRV 240

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  675 NGPllHHWLQAGDILH-RVLCLSQSEG----RVLLCRKPAlvstvegGQDPKNF--SEIHPGMLLIGFVKSIKDYGVFIQ 747
Cdd:PRK13806   241 QKA--DEAVSVGDTVRvKVLGIERAKKgkglRISLSIKQA-------GGDPWDTvgDRLKAGDKVTGKVVRLAPFGAFVE 311

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|..
gi 2462517972  748 FPSGLSGLAPKAIMS-DKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:PRK13806   312 ILPGIEGLVHVSEMSwTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLR 363
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 453-520 2.45e-04

S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240212 [Multi-domain]  Cd Length: 68  Bit Score: 41.13  E-value: 2.45e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462517972  453 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMT 520
Cdd:cd05707      1 GDVVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
1033-1093 2.59e-04

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 42.38  E-value: 2.59e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517972 1033 LSIGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHI----LDDVPEgtspttKLKVGKTVTARVI 1093
Cdd:PRK07252     1 MKIGDKLKGTITGIKPYGAFVALENGTTGLIHISEIktgfIDNIHQ------LLKVGEEVLVQVV 59
S1_Rrp5_repeat_hs1_sc1 cd05693
S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1227-1288 2.74e-04

S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240198 [Multi-domain]  Cd Length: 100  Bit Score: 41.82  E-value: 2.74e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1227 LEEGEVAMGRVVKVTPNEgLTVSFPFGKIGTVSIFHMSDSYS-----------------ETP-LED-FVPQKVVRCYILS 1287
Cdd:cd05693      1 LSEGMLVLGQVKEITKLD-LVISLPNGLTGYVPITNISDAYTerleeldeeseeeddeeELPdLEDlFSVGQLVRCKVVS 79


                   .
gi 2462517972 1288 T 1288
Cdd:cd05693     80 L 80
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 1606-1757 2.80e-04

Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures];


Pssm-ID: 444034 [Multi-domain]  Cd Length: 155  Bit Score: 43.41  E-value: 2.80e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1606 ADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTISFREEQEKLNVWVALLNLENMygsQESLtKVFERA 1685
Cdd:COG5010      5 EGFDRLPLYLLLLTKLRTLVEKYEAALAGANNTKEDELAAAGRDKLAKAFAIESPSDNLYNKLGDF---EESL-ALLEQA 80

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462517972 1686 VQYNEPL-KVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLP 1757
Cdd:COG5010     81 LQLDPNNpELYYNLALLYSRSGDKDEAKEYYEKALALSPDNPNAYSNLAALLLSLGQDDEAKAALQRALGTSP 153
S1_RPS1_repeat_ec6 cd05691
S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 734-798 3.19e-04

S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240196 [Multi-domain]  Cd Length: 73  Bit Score: 40.72  E-value: 3.19e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517972  734 GFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:cd05691      6 GKVTEVDAKGATVKLGDGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIK 70
S1_PNPase cd04472
S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a ...
 547-597 3.35e-04

S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.


Pssm-ID: 239918 [Multi-domain]  Cd Length: 68  Bit Score: 40.60  E-value: 3.35e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2462517972  547 GFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVL 597
Cdd:cd04472      6 GKVVKIKDFGAFVEILPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVI 56
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 547-609 3.45e-04

S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240212 [Multi-domain]  Cd Length: 68  Bit Score: 40.74  E-value: 3.45e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462517972  547 GFIIRVKDYGCIVKFYNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLS 609
Cdd:cd05707      6 GFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 1160-1220 3.59e-04

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 40.44  E-value: 3.59e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517972 1160 NVVKKWLEVEIAPDIRGRIPLllTSLSFKVLKHPDKKFRVGQALRATVVGPDSSKTFLCLS 1220
Cdd:cd00164      7 SITKFGVFVELEDGVEGLVHI--SELSDKFVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 186-256 3.69e-04

S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 40.69  E-value: 3.69e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517972  186 PGMLLTGTVSSLEDHGYLVDIG-VDGtraflpLLKAQE--YIRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLS 256
Cdd:cd05688      1 EGDVVEGTVKSITDFGAFVDLGgVDG------LLHISDmsWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
S1_Rrp5_repeat_sc10 cd05706
S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 726-798 3.78e-04

S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240211 [Multi-domain]  Cd Length: 73  Bit Score: 40.70  E-value: 3.78e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462517972  726 IHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:cd05706      1 LKVGDILPGRVTKVNDRYVLVQLGNKVTGPSFITDALDDYSEALPYKFKKNDIVRACVLSVDVPNKKIALSLR 73
S1_RPS1_repeat_hs4 cd05692
S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 1036-1094 3.86e-04

S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240197 [Multi-domain]  Cd Length: 69  Bit Score: 40.35  E-value: 3.86e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517972 1036 GDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDvpEGTSPTTKLKVGKTVTARVIG 1094
Cdd:cd05692      1 GSVVEGTVTRLKPFGAFVELGGGISGLVHISQIAHK--RVKDVKDVLKEGDKVKVKVLS 57
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
1035-1093 4.64e-04

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 44.94  E-value: 4.64e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517972 1035 IGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPEgtSPTTKLKVGKTVTARVI 1093
Cdd:PRK00087   562 VGSIVLGKVVRIAPFGAFVELEPGVDGLVHISQISWKRID--KPEDVLSEGEEVKAKIL 618
PRK08582 PRK08582
RNA-binding protein S1;
726-789 5.48e-04

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 41.94  E-value: 5.48e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517972  726 IHPGMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEE 789
Cdd:PRK08582     3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVLNVEDD 66
S1_RPS1_repeat_ec5 cd05690
S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 542-608 5.97e-04

S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240195 [Multi-domain]  Cd Length: 69  Bit Score: 40.17  E-value: 5.97e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462517972  542 GLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELS-TEYIPDPERVFYTGQVVKVVVLNCEPSKERMLL 608
Cdd:cd05690      1 GTVVSGKIKSITDFGIFVGLDGGIDGLVHISDISwTQRVRHPSEIYKKGQEVEAVVLNIDVERERISL 68
S1_Rrp5_repeat_hs5 cd05697
S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and ...
 729-797 6.52e-04

S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240202 [Multi-domain]  Cd Length: 69  Bit Score: 39.91  E-value: 6.52e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517972  729 GMLLIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSL 797
Cdd:cd05697      1 GQVVKGTIRKLRPSGIFVKLSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPERKRLVLTL 69
S1_Tex cd05685
S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has ...
 453-517 6.57e-04

S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.


Pssm-ID: 240190 [Multi-domain]  Cd Length: 68  Bit Score: 39.91  E-value: 6.57e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517972  453 GAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKL 517
Cdd:cd05685      1 GMVLEGVVTNVTDFGAFVDIGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDEERGRI 65
PTZ00121 PTZ00121
MAEBL; Provisional
 1402-1611 7.90e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 44.75  E-value: 7.90e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1402 KPDVLSASLEGQLTKQEERKTEAEERDQKGEKKNQKRNE--KKNQKGQEEVEMPSKEKQQPQKPQAQKRGGRECRESGSE 1479
Cdd:PTZ00121  1634 KVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEdkKKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAE 1713

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1480 QERVSKKPKKAglSEEDDSLVDVYYREGKEE---AEETNVLPKEK----QTKPAEAPRLQLSSGFAWNV---GLDSLTPA 1549
Cdd:PTZ00121  1714 EKKKAEELKKA--EEENKIKAEEAKKEAEEDkkkAEEAKKDEEEKkkiaHLKKEEEKKAEEIRKEKEAVieeELDEEDEK 1791

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517972 1550 LPPLAESsdSEEDEKPHQATQIKKSKKERELEKQKAEKELSRIEEALMDPGRQPESADDFDR 1611
Cdd:PTZ00121  1792 RRMEVDK--KIKDIFDNFANIIEGGKEGNLVINDSKEMEDSAIKEVADSKNMQLEEADAFEK 1851
rpsA PRK06676
30S ribosomal protein S1; Reviewed
 170-307 8.89e-04

30S ribosomal protein S1; Reviewed


Pssm-ID: 235851 [Multi-domain]  Cd Length: 390  Bit Score: 43.71  E-value: 8.89e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  170 LNPKNVNRVLSAEA----------------LKPGMLLTGTVSSLEDHGYLVDIG-VDGtraflpLLKAQE--YIRQKNKG 230
Cdd:PRK06676   160 LDPEKNRVILSRRAvveeeraakkeellssLKEGDVVEGTVARLTDFGAFVDIGgVDG------LVHISElsHERVEKPS 233

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517972  231 AKLKVGQYLNCIVEKVKGNGGVVSLSVGhsevstaiATEQQSWNL--NNLLPGLVVKAQVQKVTPFGLtlnFLTFFTGV 307
Cdd:PRK06676   234 EVVSVGQEVEVKVLSIDWETERISLSLK--------DTLPGPWEGveEKLPEGDVIEGTVKRLTDFGA---FVEVLPGV 301
S1_Rrp5_repeat_hs13 cd05704
S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 728-798 9.46e-04

S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240209 [Multi-domain]  Cd Length: 72  Bit Score: 39.64  E-value: 9.46e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2462517972  728 PGMLLIGFV-KSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVtnVDEEKQRMLLSLR 798
Cdd:cd05704      3 EGAVTLGMVtKVIPHSGLTVQLPFGKTGLVSIFHLSDSYTENPLEGFKPGKIVRCCI--LSKKDGKYQLSLR 72
PRK12269 PRK12269
bifunctional cytidylate kinase/ribosomal protein S1; Provisional
 540-798 1.10e-03

bifunctional cytidylate kinase/ribosomal protein S1; Provisional


Pssm-ID: 105491 [Multi-domain]  Cd Length: 863  Bit Score: 43.93  E-value: 1.10e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  540 KPGLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELSTeyipdPERvfyTGQVVKVVVLNCEPSKERMllsFKLSSDPEPK 619
Cdd:PRK12269   320 EPGSVRMGTVVQVNAGTVFVDIGGKSEGRVPVEEFEA-----PPK---AGDGVRVYVERVTPYGPEL---SKTKADRLGL 388

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  620 KEPAGHSQKKGKAINiGQLVDvkvLEKTKDGLEVAvLPHNIRAFLPTSHLSDHVANGPLLHHWLQAGDILHRVLCLSQSE 699
Cdd:PRK12269   389 KVKLRDAERDGTPVE-GRIVR---LTEKKSGFEVD-LGAGMMAFLPISQSDCQKVDAPESLIGLTSKFYIERISQSKQHR 463

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  700 GR--VLLCRKPALVSTVEGGQDpKNFSEIHPGMLLIGFVKSIKDYGVFIQFpSGLSGLAPKAIMSDKFVTSTSDHFVEGQ 777
Cdd:PRK12269   464 GNdnIVINRRRYLEERARQARE-EFFNSVHIEDSVSGVVKSFTSFGAFIDL-GGFDGLLHVNDMSWGHVARPREFVKKGQ 541

                          250       260
                   ....*....|....*....|.
gi 2462517972  778 TVAAKVTNVDEEKQRMLLSLR 798
Cdd:PRK12269   542 TIELKVIRLDQAEKRINLSLK 562
PTZ00121 PTZ00121
MAEBL; Provisional
 1416-1726 1.33e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 43.98  E-value: 1.33e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1416 KQEERKTEAEERDQKGE--KKNQKRNEKKNQKGQEEVEMPSKEKQQPQKPQAQKRGGRECRESGSEQERVSKKPKKAglS 1493
Cdd:PTZ00121  1323 KAEEAKKKADAAKKKAEeaKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKADAAKKKAEEKKKADEAKKK--A 1400

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1494 EEDDSLVDVYYR--EGKEEAEETNVLPKEK------QTKPAEAPRLQLSSGFAWNVglDSLTPALPPLAESSDSEE-DEK 1564
Cdd:PTZ00121  1401 EEDKKKADELKKaaAAKKKADEAKKKAEEKkkadeaKKKAEEAKKADEAKKKAEEA--KKAEEAKKKAEEAKKADEaKKK 1478

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1565 PHQATQIKKSKKERELEKQKAEkELSRIEEA--LMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAV 1642
Cdd:PTZ00121  1479 AEEAKKADEAKKKAEEAKKKAD-EAKKAAEAkkKADEAKKAEEAKKADEAKKAEEAKKADEAKKAEEKKKADELKKAEEL 1557

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1643 --AERALKTISFREEQEKlnvwvallnlENMYGSQESLTKVFERAvQYNEPLKVFLHLADIYAKSEKFQEAGELYNRMLK 1720
Cdd:PTZ00121  1558 kkAEEKKKAEEAKKAEED----------KNMALRKAEEAKKAEEA-RIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELK 1626


                   ....*.
gi 2462517972 1721 RFRQEK 1726
Cdd:PTZ00121  1627 KAEEEK 1632
rpsA PRK13806
30S ribosomal protein S1; Provisional
 1168-1350 1.34e-03

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 43.56  E-value: 1.34e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1168 VEIAPDIRGRIPLllTSLSFKVLKHPDKKFRVGQALRATVVGPDSSK----TFLCLSL---------TGPHKLEEGEVAM 1234
Cdd:PRK13806   220 VELAPGVEGMVHI--SELSWSRVQKADEAVSVGDTVRVKVLGIERAKkgkgLRISLSIkqaggdpwdTVGDRLKAGDKVT 297

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1235 GRVVKVTPNeGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFV-PQKVVRCYI--LSTADNVLTLSLRSSRTnpetkskve 1311
Cdd:PRK13806   298 GKVVRLAPF-GAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVaPGDAVAVKIkdIDPAKRRISLSLRDAEG--------- 367

                          170       180       190
                   ....*....|....*....|....*....|....*....
gi 2462517972 1312 DPEINSIQDIKEGQLLRGYVGSIQPHGVFFRLGPSVVGL 1350
Cdd:PRK13806   368 DPWADVAERFAPGTTVTGTVEKRAQFGLFVNLAPGVTGL 406
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 88-169 1.37e-03

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 38.90  E-value: 1.37e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972   88 GCVKEVNELELVISLPNGLQGFVQVTEICDAYTKklneqvtqeqplkdllHLPELFSPGMLVRCVVSSLgitDRGKKSVK 167
Cdd:cd00164      3 GKVVSITKFGVFVELEDGVEGLVHISELSDKFVK----------------DPSEVFKVGDEVEVKVLEV---DPEKGRIS 63


                   ..
gi 2462517972  168 LS 169
Cdd:cd00164     64 LS 65
TadD COG5010
Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, ...
 1696-1826 1.39e-03

Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures];


Pssm-ID: 444034 [Multi-domain]  Cd Length: 155  Bit Score: 41.10  E-value: 1.39e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1696 LHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPskEHVDVIAKFAQLEFQL 1775
Cdd:COG5010     24 VEKYEAALAGANNTKEDELAAAGRDKLAKAFAIESPSDNLYNKLGDFEESLALLEQALQLDP--NNPELYYNLALLYSRS 101

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2462517972 1776 GDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVIHLS 1826
Cdd:COG5010    102 GDKDEAKEYYEKALALSPDNPNAYSNLAALLLSLGQDDEAKAALQRALGTS 152
TPR COG0457
Tetratricopeptide (TPR) repeat [General function prediction only];
1595-1783 1.41e-03

Tetratricopeptide (TPR) repeat [General function prediction only];


Pssm-ID: 440225 [Multi-domain]  Cd Length: 245  Bit Score: 42.30  E-value: 1.41e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1595 ALMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTisfreeqeKLNVWVALLNLENMYGS 1674
Cdd:COG0457     51 AYLRLGRYEEALADYEQALELDPDDAEALNNLGLALQALGRYEEALEDYDKALEL--------DPDDAEALYNLGLALLE 122

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1675 QESLTK---VFERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNrmlKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQ 1750
Cdd:COG0457    123 LGRYDEaieAYERALELDpDDADALYNLGIALEKLGRYEEALELLE---KLEAAALAALLAAALGEAALALAAAEVLLAL 199

                          170       180       190
                   ....*....|....*....|....*....|...
gi 2462517972 1751 RALECLPSKEHVDVIAKFAQLEFQLGDAERAKA 1783
Cdd:COG0457    200 LLALEQALRKKLAILTLAALAELLLLALALLLA 232
S1_like cd00164
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 190-256 1.50e-03

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


Pssm-ID: 238094 [Multi-domain]  Cd Length: 65  Bit Score: 38.90  E-value: 1.50e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462517972  190 LTGTVSSLEDHGYLVDIGvDGTRAFLPLLKAQEYiRQKNKGAKLKVGQYLNCIVEKVKGNGGVVSLS 256
Cdd:cd00164      1 VTGKVVSITKFGVFVELE-DGVEGLVHISELSDK-FVKDPSEVFKVGDEVEVKVLEVDPEKGRISLS 65
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 1499-1794 1.51e-03

putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.


Pssm-ID: 274350 [Multi-domain]  Cd Length: 899  Bit Score: 43.53  E-value: 1.51e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1499 LVDVYYREGKEEaEETNVLPKEKQTKPAE-APRLQLSSGFawnVGLDSLTPALPPLAESSDSEEDEKphQATQIKKSKke 1577
Cdd:TIGR02917  539 LAGLYLRTGNEE-EAVAWLEKAAELNPQEiEPALALAQYY---LGKGQLKKALAILNEAADAAPDSP--EAWLMLGRA-- 610

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1578 relekQKAEKELSRIEEAlmdpgrqpesaddFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTIS-FREEQ 1656
Cdd:TIGR02917  611 -----QLAAGDLNKAVSS-------------FKKLLALQPDSALALLLLADAYAVMKNYAKAITSLKRALELKPdNTEAQ 672

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1657 EKLnvwVALLNLENMYGSQESLTKVFEraVQYNEPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVwIKYGAFL 1736
Cdd:TIGR02917  673 IGL---AQLLLAAKRTESAKKIAKSLQ--KQHPKAALGFELEGDLYLRQKDYPAAIQAYRKALKRAPSSQNA-IKLHRAL 746

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517972 1737 LRRSQAAASHRVLQRALeclpsKEHV-DVIAKFAQLEFQLGDAERAKAI--FENTLSTYPK 1794
Cdd:TIGR02917  747 LASGNTAEAVKTLEAWL-----KTHPnDAVLRTALAELYLAQKDYDKAIkhYQTVVKKAPD 802
S1_Rrp5_repeat_hs11_sc8 cd05702
S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the ...
 90-134 1.72e-03

S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240207 [Multi-domain]  Cd Length: 70  Bit Score: 38.73  E-value: 1.72e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 2462517972   90 VKEVNELELVISLPNGLQGFVQVTEICDAYTkklneqvTQEQPLK 134
Cdd:cd05702      8 VKSVKPTQLNVQLADNVHGRIHVSEVFDEWP-------DGKNPLS 45
rpsA PRK07899
30S ribosomal protein S1; Reviewed
 443-523 2.28e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 236126 [Multi-domain]  Cd Length: 486  Bit Score: 42.72  E-value: 2.28e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  443 QYLRYHDIepGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVLLCDPEAKKLMMTLK 522
Cdd:PRK07899   286 QFARTHAI--GQIVPGKVTKLVPFGAFVRVEEGIEGLVHISELAERHVEVPEQVVQVGDEVFVKVIDIDLERRRISLSLK 363


                   .
gi 2462517972  523 K 523
Cdd:PRK07899   364 Q 364
PilF COG3063
Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];
1630-1721 2.36e-03

Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures];


Pssm-ID: 442297 [Multi-domain]  Cd Length: 94  Bit Score: 39.00  E-value: 2.36e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1630 HLQATEIEKARAVAERALKTisfreeqeKLNVWVALLNLENMYGSQESltkvFERAVQYNEPLK-------VFLHLADIY 1702
Cdd:COG3063      2 YLKLGDLEEAEEYYEKALEL--------DPDNADALNNLGLLLLEQGR----YDEAIALEKALKldpnnaeALLNLAELL 69

                           90
                   ....*....|....*....
gi 2462517972 1703 AKSEKFQEAGELYNRMLKR 1721
Cdd:COG3063     70 LELGDYDEALAYLERALEL 88
PTZ00121 PTZ00121
MAEBL; Provisional
 1413-1594 2.46e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 43.21  E-value: 2.46e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1413 QLTKQEE-RKTE----AEERDQKGEKKNQKRNEKKNQKGQEEVEMPSKEKQQPQKPQAQKRGGRECRESGSEQERVSKKP 1487
Cdd:PTZ00121  1556 ELKKAEEkKKAEeakkAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKV 1635

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1488 KKAGLSEEDdslvDVYYREGKEEAEETNVLPKEKQTKPAEAPRLQlssgfawnvgldsltpalpplAESSDSEEDEKPHQ 1567
Cdd:PTZ00121  1636 EQLKKKEAE----EKKKAEELKKAEEENKIKAAEEAKKAEEDKKK---------------------AEEAKKAEEDEKKA 1690

                          170       180       190
                   ....*....|....*....|....*....|....*..
gi 2462517972 1568 ATQIKKS----------KKERELEKQKAEkELSRIEE 1594
Cdd:PTZ00121  1691 AEALKKEaeeakkaeelKKKEAEEKKKAE-ELKKAEE 1726
S1_RPS1_repeat_ec2_hs2 cd04465
S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 636-707 2.59e-03

S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 239911 [Multi-domain]  Cd Length: 67  Bit Score: 38.21  E-value: 2.59e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517972  636 GQLVDVKVLEKTKDGLEVAVlpHNIRAFLPTSHLSD-HVAN-GPLLHHWLQAgdilhRVLCLSQSEGRVLLCRK 707
Cdd:cd04465      1 GEIVEGKVTEKVKGGLIVDI--EGVRAFLPASQVDLrPVEDlDEYVGKELKF-----KIIEIDRERNNIVLSRR 67
S1_RPS1_repeat_ec4 cd05689
S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 542-608 3.11e-03

S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240194 [Multi-domain]  Cd Length: 72  Bit Score: 37.94  E-value: 3.11e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462517972  542 GLQTHGFIIRVKDYGCIVKFYNNVQGLVPKHELS-TEYIPDPERVFYTGQVVKVVVLNCEPSKERMLL 608
Cdd:cd05689      4 GTRLFGKVTNLTDYGCFVELEEGVEGLVHVSEMDwTNKNIHPSKVVSLGDEVEVMVLDIDEERRRISL 71
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 1749-1830 3.21e-03

Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443378 [Multi-domain]  Cd Length: 131  Bit Score: 39.60  E-value: 3.21e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1749 LQRALECLPskEHVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDVRDIFERVihLSLA 1828
Cdd:COG4235      6 LRQALAANP--NDAEGWLLLGRAYLRLGRYDEALAAYEKALRLDPDNADALLDLAEALLAAGDTEEAEELLERA--LALD 81


                   ..
gi 2462517972 1829 PK 1830
Cdd:COG4235     82 PD 83
rpsA PRK13806
30S ribosomal protein S1; Provisional
 66-306 3.24e-03

30S ribosomal protein S1; Provisional


Pssm-ID: 237516 [Multi-domain]  Cd Length: 491  Bit Score: 42.02  E-value: 3.24e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972   66 KSAREKFeilsVESLCEGMRILGCVKEVNELELVISLPNGLQGFVQVTEICDAYTKKLNEQVtqeqplkdllhlpelfSP 145
Cdd:PRK13806   190 KEALEAF----METVKEGDVVEGTVTRLAPFGAFVELAPGVEGMVHISELSWSRVQKADEAV----------------SV 249

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  146 GMLVRcvVSSLGITDRGK-KSVKLSLNPKNV-----NRVlsAEALKPGMLLTGTVSSLEDHGYLVDI--GVDGtrafLPL 217
Cdd:PRK13806   250 GDTVR--VKVLGIERAKKgKGLRISLSIKQAggdpwDTV--GDRLKAGDKVTGKVVRLAPFGAFVEIlpGIEG----LVH 321

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  218 LKAQEYIRQKNK-GAKLKVGQYLNCIVEKVKGNGGVVSLSVGHSEVSTAIATEQQswnlnnLLPGLVVKAQVQKVTPFGL 296
Cdd:PRK13806   322 VSEMSWTRRVNKpEDVVAPGDAVAVKIKDIDPAKRRISLSLRDAEGDPWADVAER------FAPGTTVTGTVEKRAQFGL 395

                          250
                   ....*....|
gi 2462517972  297 TLNFLTFFTG 306
Cdd:PRK13806   396 FVNLAPGVTG 405
PRK08582 PRK08582
RNA-binding protein S1;
450-508 3.60e-03

RNA-binding protein S1;


Pssm-ID: 236305 [Multi-domain]  Cd Length: 139  Bit Score: 39.63  E-value: 3.60e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517972  450 IEPGAVVKGTVLTIKSYGMLVKVGEQMRGLVPPMHLADILMKNPEKKYHIGDEVKCRVL 508
Cdd:PRK08582     3 IEVGSKLQGKVTGITNFGAFVELPEGKTGLVHISEVADNYVKDINDHLKVGDEVEVKVL 61
PRK00087 PRK00087
bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;
1032-1394 3.63e-03

bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1;


Pssm-ID: 234623 [Multi-domain]  Cd Length: 647  Bit Score: 42.24  E-value: 3.63e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1032 TLSIGDMVTGTVKSIKPTHVVVTL---EDGIIGCIHASHilddvPEGTSPTTKLKVGKTVTARVIGGRDmktfkylpish 1108
Cdd:PRK00087   299 QIRRGDIVKGTVVSVNENEVFVDVgykSEGVIPLRELTL-----DEISSLKESVKVGDEIEVKVLKLED----------- 362

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1109 prfvrtipelsvrpselEDGHTALN---THSVSPMEKIKQ-YQAGQTVTCFLKKynVVKKWLEVEIApDIRGRIPLLLTS 1184
Cdd:PRK00087   363 -----------------EDGYVVLSkkeADREKAWKELEEaFENGEPVKGKVKE--VVKGGLLVDYG-GVRAFLPASHVE 422

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1185 LSFKvlkhPDKKFRVGQALRATVVGPD---------SSKTFLCLSLTGPHK-----LEEGEVAMGRVVKVTPNeGLtvsf 1250
Cdd:PRK00087   423 LGYV----EDLSEYKGQELEVKIIEFNrkrrkkvvlSRKAILEEEKEKKKEetwnsLEEGDVVEGEVKRLTDF-GA---- 493

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1251 pFGKIGTVS-IFHMSD---SYSETPLEDFVPQKVVRCYILSTADNVLTLSLrsSRtnpetKSKVEDPEINSIQDIKEGQL 1326
Cdd:PRK00087   494 -FVDIGGVDgLLHVSEiswGRVEKPSDVLKVGDEIKVYILDIDKENKKLSL--SL-----KKLLPDPWENVEEKYPVGSI 565

                          330       340       350       360       370       380       390
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517972 1327 LRGYVGSIQPHGVFFRLGPSVVGLARYSHVSQH---SPSKKalynkhLPEGKLLTARVLRLNHQKNLVELS 1394
Cdd:PRK00087   566 VLGKVVRIAPFGAFVELEPGVDGLVHISQISWKridKPEDV------LSEGEEVKAKILEVDPEEKRIRLS 630
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 1572-1794 5.02e-03

putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.


Pssm-ID: 274350 [Multi-domain]  Cd Length: 899  Bit Score: 41.99  E-value: 5.02e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1572 KKSKKERELEKQ--------KAEKELSRIEealMDPGRQPESADDFDRLVLSSPNSSILWLQYMAFHLQATEIEKARAVA 1643
Cdd:TIGR02917  480 DLAKAREAFEKAlsiepdffPAAANLARID---IQEGNPDDAIQRFEKVLTIDPKNLRAILALAGLYLRTGNEEEAVAWL 556

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1644 ERALKTISfREEQEKLNVWVALLNLENMygsQESLTKVFERAVQYNEPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFR 1723
Cdd:TIGR02917  557 EKAAELNP-QEIEPALALAQYYLGKGQL---KKALAILNEAADAAPDSPEAWLMLGRAQLAAGDLNKAVSSFKKLLALQP 632

                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517972 1724 QEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPskEHVDVIAKFAQLEFQLGDAERAKAIFENTLSTYPK 1794
Cdd:TIGR02917  633 DSALALLLLADAYAVMKNYAKAITSLKRALELKP--DNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQHPK 701
DUF612 pfam04747
Protein of unknown function, DUF612; This family includes several uncharacterized proteins ...
 1399-1599 5.16e-03

Protein of unknown function, DUF612; This family includes several uncharacterized proteins from Caenorhabditis elegans.


Pssm-ID: 282585 [Multi-domain]  Cd Length: 511  Bit Score: 41.59  E-value: 5.16e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1399 DTGKPDVLSASLEGQLTKQEERKTEAEERDQKGEKKNQKRNEKKNQKGQEEVEMPSKEKQQPQKPQAQkrggRECRESGS 1478
Cdd:pfam04747   49 DQRKEAFASLELTEQPQQVEKVKKSEKKKAQKQIAKDHEAEQKVNAKKAAEKEARRAEAEAKKRAAQE----EEHKQWKA 124

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1479 EQERVSKKPKKaglseEDDSLVDVYYREGKEEAEETNVLPKEKQTKPAEAPRLQLSSGFAWNVGLD-SLTPALPPLAESS 1557
Cdd:pfam04747  125 EQERIQKEQEK-----KEADLKKLQAEKKKEKAVKAEKAEKAEKTKKASTPAPVEEEIVVKKVANDrSAAPAPEPKTPTN 199

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|..
gi 2462517972 1558 DSEEDEKPHQATQIKKSKKERELEKQKAEKELSRIEEALMDP 1599
Cdd:pfam04747  200 TPAEPAEQVQEITGKKNKKNKKKSESEATAAPASVEQVVEQP 241
PTZ00121 PTZ00121
MAEBL; Provisional
 1413-1658 5.29e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 42.05  E-value: 5.29e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1413 QLTKQEERKTEAEERDQKGEKK--NQKRNEKKNQKGQEEVEMPSKEKQQPQKPQAQKRGGRECR---ESGSEQERVSKKP 1487
Cdd:PTZ00121  1501 EAKKAAEAKKKADEAKKAEEAKkaDEAKKAEEAKKADEAKKAEEKKKADELKKAEELKKAEEKKkaeEAKKAEEDKNMAL 1580

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1488 KKAGLSEE-----DDSLVDVYYREGKEEAEETNVLPKEK----QTKPAEAPRLQLSSgfawnvgLDSLTPALPPLAESSD 1558
Cdd:PTZ00121  1581 RKAEEAKKaeearIEEVMKLYEEEKKMKAEEAKKAEEAKikaeELKKAEEEKKKVEQ-------LKKKEAEEKKKAEELK 1653

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1559 SEEDEKPHQATQIKKSKKE---RELEKQKAEKELSRIEEALMDPGRQPESADDFDRLVLSSPNssilwlqymafhlQATE 1635
Cdd:PTZ00121  1654 KAEEENKIKAAEEAKKAEEdkkKAEEAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKK-------------KAEE 1720

                          250       260
                   ....*....|....*....|...
gi 2462517972 1636 IEKARAVAERALKTISFREEQEK 1658
Cdd:PTZ00121  1721 LKKAEEENKIKAEEAKKEAEEDK 1743
S1_Rrp5_repeat_sc11 cd05707
S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S ...
 1324-1394 5.31e-03

S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 240212 [Multi-domain]  Cd Length: 68  Bit Score: 37.27  E-value: 5.31e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517972 1324 GQLLRGYVGSIQPHGVFFRLGPSVVGLARyshVSQHSPSKKALYNKHLPEGKLLTARVLRLNHQKNLVELS 1394
Cdd:cd05707      1 GDVVRGFVKNIANNGVFVTLGRGVDARVR---VSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIEMT 68
Spy COG3914
Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational ...
 1577-1834 5.64e-03

Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443119 [Multi-domain]  Cd Length: 658  Bit Score: 41.52  E-value: 5.64e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1577 ERELEKQKAEKELSRIEEALMDPGRQPESADDFDRLVLSSPNSSILWLqYMAFHLQATE-IEKARAVAERALKtisfree 1655
Cdd:COG3914     69 AAAAALLLLAALLELAALLLQALGRYEEALALYRRALALNPDNAEALF-NLGNLLLALGrLEEALAALRRALA------- 140

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1656 qeklnvwvalLNLENmygsqesltkvferavqynepLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAF 1735
Cdd:COG3914    141 ----------LNPDF---------------------AEAYLNLGEALRRLGRLEEAIAALRRALELDPDNAEALNNLGNA 189

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1736 LLRRSQAAASHRVLQRALECLPskEHVDVIAKFAQLEFQLGDAERAkAIFENTLSTYPKRTDVWSVYIDMTIKHGSQKDV 1815
Cdd:COG3914    190 LQDLGRLEEAIAAYRRALELDP--DNADAHSNLLFALRQACDWEVY-DRFEELLAALARGPSELSPFALLYLPDDDPAEL 266

                          250       260
                   ....*....|....*....|..
gi 2462517972 1816 RDI---FERVIHLSLAPKRMKF 1834
Cdd:COG3914    267 LALaraWAQLVAAAAAPELPPP 288
PEP_TPR_lipo TIGR02917
putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly ...
 1610-1793 6.04e-03

putative PEP-CTERM system TPR-repeat lipoprotein; This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.


Pssm-ID: 274350 [Multi-domain]  Cd Length: 899  Bit Score: 41.61  E-value: 6.04e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1610 DRLVLSSPNSSILWLQYMAFHLQATEIEKARAVAERALKTisfreEQEKLNvwvALLNLENMYGSQESL---TKVFERAV 1686
Cdd:TIGR02917  455 KKLEKKQPDNASLHNLLGAIYLGKGDLAKAREAFEKALSI-----EPDFFP---AAANLARIDIQEGNPddaIQRFEKVL 526

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1687 QYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLP-SKEHVDV 1764
Cdd:TIGR02917  527 TIDpKNLRAILALAGLYLRTGNEEEAVAWLEKAAELNPQEIEPALALAQYYLGKGQLKKALAILNEAADAAPdSPEAWLM 606

                          170       180
                   ....*....|....*....|....*....
gi 2462517972 1765 IAKfAQLefQLGDAERAKAIFENTLSTYP 1793
Cdd:TIGR02917  607 LGR-AQL--AAGDLNKAVSSFKKLLALQP 632
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 1226-1297 6.57e-03

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 37.57  E-value: 6.57e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2462517972 1226 KLEEGEVAMGRVVKVTPNeGLTVSFPFGKIGTVSIFHMSDSYSETPLEDFVPQKVVRCYILS--TADNVLTLSL 1297
Cdd:cd04461     11 DLKPGMVVHGYVRNITPY-GVFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSvdEEKQRFLLSL 83
PRK07400 PRK07400
30S ribosomal protein S1; Reviewed
 660-796 6.70e-03

30S ribosomal protein S1; Reviewed


Pssm-ID: 180960 [Multi-domain]  Cd Length: 318  Bit Score: 40.94  E-value: 6.70e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972  660 IRAFLPTSHLSDHVANGPLLHHWLQAgdilhRVLCLSQSEGRVLLCRKPALVStveggqdpKNFSEIHPGMLLIGFVKSI 739
Cdd:PRK07400   141 LRGFIPGSHISTRKPKEELVGEELPL-----KFLEVDEERNRLVLSHRRALVE--------RKMNRLEVGEVVVGTVRGI 207

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 2462517972  740 KDYGVFIQFpSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLS 796
Cdd:PRK07400   208 KPYGAFIDI-GGVSGLLHISEISHEHIETPHSVFNVNDEMKVMIIDLDAERGRISLS 263
NrfG COG4235
Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, ...
 1680-1767 6.98e-03

Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443378 [Multi-domain]  Cd Length: 131  Bit Score: 38.45  E-value: 6.98e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517972 1680 KVFERAVQYN-EPLKVFLHLADIYAKSEKFQEAGELYNRMLKRFRQEKAVWIKYGAFLLRRSQAAASHRVLQRALECLPS 1758
Cdd:COG4235     38 AAYEKALRLDpDNADALLDLAEALLAAGDTEEAEELLERALALDPDNPEALYLLGLAAFQQGDYAEAIAAWQKLLALLPA 117


                   ....*....
gi 2462517972 1759 KEHVDVIAK 1767
Cdd:COG4235    118 DAPARLLEA 126
PRK07252 PRK07252
S1 RNA-binding domain-containing protein;
732-798 8.05e-03

S1 RNA-binding domain-containing protein;


Pssm-ID: 180908 [Multi-domain]  Cd Length: 120  Bit Score: 38.14  E-value: 8.05e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2462517972  732 LIGFVKSIKDYGVFIQFPSGLSGLAPKAIMSDKFVTSTSDHFVEGQTVAAKVTNVDEEKQRMLLSLR 798
Cdd:PRK07252     7 LKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSLR 73
S1_RPS1_repeat_ec3 cd05688
S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ...
 541-609 9.00e-03

S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.


Pssm-ID: 240193 [Multi-domain]  Cd Length: 68  Bit Score: 36.45  E-value: 9.00e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517972  541 PGLQTHGFIIRVKDYGCIVKFyNNVQGLVPKHELSTEYIPDPERVFYTGQVVKVVVLNCEPSKERMLLS 609
Cdd:cd05688      1 EGDVVEGTVKSITDFGAFVDL-GGVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDKERKRISLG 68
S1_Rrp5_repeat_hs8_sc7 cd04461
S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 ...
 1033-1093 9.08e-03

S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.


Pssm-ID: 239908 [Multi-domain]  Cd Length: 83  Bit Score: 37.18  E-value: 9.08e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517972 1033 LSIGDMVTGTVKSIKPTHVVVTLEDGIIGCIHASHILDDVPegTSPTTKLKVGKTVTARVI 1093
Cdd:cd04461     12 LKPGMVVHGYVRNITPYGVFVEFLGGLTGLAPKSYISDEFV--TDPSFGFKKGQSVTAKVT 70
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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